Single Cell Quantification

-Single cell quantification with skimage

# HDI quantification
# import custom modules
from miaaim.quant.quantification import HDIquantification

# import external modules
from pathlib import Path
import pandas as pd
import os
import numpy as np
import skimage.io
import nibabel as nib
from tqdm import tqdm

import skimage.filters.edges as ed
import scipy.ndimage
from miaaim.io.imread import _import

# check versions and environment executable
import sys
sys.version
sys.executable

'/opt/conda/envs/miaaim-dev/bin/python'

# n-dimensional filter weights
SOBEL_EDGE = np.array([1, 0, -1])
SOBEL_SMOOTH = np.array([1, 2, 1]) / 4

def sobel(image, mask=None, *, axis=None, mode='reflect', cval=0.0):
    """Find edges in an image using the Sobel filter.
    Parameters
    ----------
    image : array
        The input image.
    mask : array of bool, optional
        Clip the output image to this mask. (Values where mask=0 will be set
        to 0.)
    axis : int or sequence of int, optional
        Compute the edge filter along this axis. If not provided, the edge
        magnitude is computed. This is defined as::
            sobel_mag = np.sqrt(sum([sobel(image, axis=i)**2
                                     for i in range(image.ndim)]) / image.ndim)
        The magnitude is also computed if axis is a sequence.
    mode : str or sequence of str, optional
        The boundary mode for the convolution. See `scipy.ndimage.convolve`
        for a description of the modes. This can be either a single boundary
        mode or one boundary mode per axis.
    cval : float, optional
        When `mode` is ``'constant'``, this is the constant used in values
        outside the boundary of the image data.
    Returns
    -------
    output : array of float
        The Sobel edge map.
    See also
    --------
    sobel_h, sobel_v : horizontal and vertical edge detection.
    scharr, prewitt, farid, skimage.feature.canny
    References
    ----------
    .. [1] D. Kroon, 2009, Short Paper University Twente, Numerical
           Optimization of Kernel Based Image Derivatives.
    .. [2] https://en.wikipedia.org/wiki/Sobel_operator
    Examples
    --------
    >>> from skimage import data
    >>> from skimage import filters
    >>> camera = data.camera()
    >>> edges = filters.sobel(camera)
    """
    output = ed._generic_edge_filter(image, smooth_weights=SOBEL_SMOOTH,
                                  axis=axis, mode=mode, cval=cval)
    output = ed._mask_filter_result(output, mask)
    return output


def sobel_h(image, mask=None):
    """Find the horizontal edges of an image using the Sobel transform.
    Parameters
    ----------
    image : 2-D array
        Image to process.
    mask : 2-D array, optional
        An optional mask to limit the application to a certain area.
        Note that pixels surrounding masked regions are also masked to
        prevent masked regions from affecting the result.
    Returns
    -------
    output : 2-D array
        The Sobel edge map.
    Notes
    -----
    We use the following kernel::
      1   2   1
      0   0   0
     -1  -2  -1
    """
    return sobel(image, mask=mask, axis=0)


def sobel_v(image, mask=None):
    """Find the vertical edges of an image using the Sobel transform.
    Parameters
    ----------
    image : 2-D array
        Image to process.
    mask : 2-D array, optional
        An optional mask to limit the application to a certain area.
        Note that pixels surrounding masked regions are also masked to
        prevent masked regions from affecting the result.
    Returns
    -------
    output : 2-D array
        The Sobel edge map.
    Notes
    -----
    We use the following kernel::
      1   0  -1
      2   0  -2
      1   0  -1
    """
    return sobel(image, mask=mask, axis=1)


def per_channel_sobel(arr, nms, sigma=2):
    """Sobel filter over each channel of 2D imaging data.

    Parameters
    ----------
    arr: numpy.ndarray with 3 axes.
        Input image consisting of c,y,x axes.

    nms: list
        Indicates names of markers in the array indexed in position 0.

    out_dir: os path
        Output directory to store resulting image.

    sigma: int
        Gaussian smoothing parameter.
    """
    # get sizes of image
    x,y,c = arr.shape
    # create array to store results
    grad_array = np.zeros((x,y,c,2))
    grad_mag_array = np.zeros((x,y,c))
    # create indexer
    i = 0
    # iterate through each gene
    for g in tqdm(nms, desc='Computing image gradients'):
        # get gene
        C_ = arr[:,:,i]
        # reshape
        C = C_.reshape(C_.shape[0],C_.shape[1])
        # apply gaussian smoothing
        if sigma is not None:
            # smooth
            C = scipy.ndimage.gaussian_filter(C,sigma=sigma)

        # compute gradient approximation with sobel filter
        grad_h = sobel_h(C)
        grad_v = sobel_v(C)
        # compute magnitude
        sobel_mag = np.sqrt(sum([i**2 for i in [grad_h,grad_v]])/2)

        # update output array with gradients
        grad_array[:,:,i,0] = grad_h
        grad_array[:,:,i,1] = grad_v
        # update output array of gradient magnitude
        grad_mag_array[:,:,i] = sobel_mag

        # update indexer
        i = i + 1

    # return
    return grad_array, grad_mag_array, list(nms)

def TMAquantification(core_name, data_folder, gradients=True, grad_sigmas=[25]):
    # set path to core folder (root_folder below)
    core_folder = data_folder.joinpath(f"{core_name}")

    # check if segmentation directory exists
    _segdir = core_folder.joinpath("segmentation/imc/hdiseg-ilastik")
    # check if the registration transformix directory exists
    _transdir = core_folder.joinpath("registration/msi-imc")

    # check if segmentation exists
    if _segdir.exists():
        # set root folder as the core folder
        root_folder = core_folder
        # set path to segmentation mask
        masks = [ core_folder.joinpath(f"segmentation/imc/hdiseg-ilastik/{core_name}_core_probabilities_mask.tiff") ]
        # set path to imc preprocessed image to quantify
        imcIm = core_folder.joinpath(f"preprocessing/imc/{core_name}_core.ome.tiff")

        # add to list of images
        imagesList = [ imcIm ]
        # create markers list
        channelsList = [ data_folder.joinpath("imc-markers.csv") ]
        # create names list
        namesList = [ "imc" ]

        # create list to store gradient magnitude images in
        grad_mags_list = []
        # check if multimodal registered data exists
        if _transdir.exists():
            # set path to imc preprocessed image to quantify
            msiIm = root_folder.joinpath(f"registration/msi-imc/transformix/{core_name}_result.nii")

            # update list with the msi data
            imagesList.append(msiIm)
            # update markers list
            channelsList.append(data_folder.joinpath("msi-markers.csv"))
            # update names list
            namesList.append("msi")

            # check if computing gradients
            if gradients:
                # read the registered msi data
                msiIm = _import.HDIreader(
                    path_to_data=msiIm,
                    path_to_markers=None,
                    flatten=False,
                    subsample=False,
                    method=None,
                    mask=None,
                    save_mem=False,
                    data=None,
                    image=None,
                    channels=None,
                    filename=None)
                # iterate over sigmas
                for s in grad_sigmas:
                    # compute gradients
                    grads, grad_magnitudes, _ = per_channel_sobel(
                        msiIm.hdi.data.image,
                        nms=range(msiIm.hdi.data.image.shape[2]),
                        sigma=s)
                    # create name for exporting gradint magnitudes
                    msiImGrad = root_folder.joinpath(f"registration/msi-imc/transformix/{core_name}_result_gradient_magnitude_{str(s)}.nii")
                    # create nifti image
                    arr = nib.Nifti1Image(grad_magnitudes.transpose(1, 0, 2), affine=np.eye(4))
                    # export gradients
                    nib.save(arr,str(msiImGrad))
                    # update list with the msi data
                    imagesList.append(msiImGrad)
                    # update markers list
                    channelsList.append(data_folder.joinpath("msi-markers.csv"))
                    # update names list
                    namesList.append(f"msi-gradient-magnitude-sigma-{str(s)}")
                    # update list of gradient magnitude images
                    grad_mags_list.append(msiImGrad)

        # create quantification instance
        quantifier = HDIquantification(root_folder=root_folder,
                    masks=masks,
                    images=imagesList,
                    channel_names=channelsList,
                    names=namesList,
                    probabilities_method="ilastik",
                    segmentation_method="hdiseg",
                    mask_props=None,
                    intensity_props=["intensity_mean"])
        # quantify
        quantifier.Quantify()
        # export documentation
        quantifier.QC()

        # remove the gradient images for storage space
        if len(grad_mags_list)>0:
            for z in grad_mags_list:
                z.unlink(missing_ok=False)

# set path to data folder
data_folder = Path("/opt/miaaim-20220912-TMA4/data")
# get list of all core names in the data folder
# check to make sure we have the core folders for only prostate samples which have
# multimodal data (here, indicated by /registration folder)
core_folders = [data_folder.joinpath(c) for c in os.listdir(data_folder) if data_folder.joinpath(c).is_dir()]
core_folders = [c for c in core_folders if Path(f"{c}/probabilities/imc/ilastik").is_dir()]

# print the size of the list of folders
print(f"NUMBER OF MASS CYTOMETRY CORES: {str(len(core_folders))}")
# iterate through data set and register
for c in core_folders:
    # register
    TMAquantification(core_name=c.name, data_folder=data_folder)

NUMBER OF MASS CYTOMETRY CORES: 61

Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [23:33<00:00,  2.01s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/preprocessing/imc/ROI010_PROSTATE_TMA001_core.ome.tiff...
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Finished ROI010_PROSTATE_TMA001_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/registration/msi-imc/transformix/ROI010_PROSTATE_TMA001_result.nii...
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Finished ROI010_PROSTATE_TMA001_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/registration/msi-imc/transformix/ROI010_PROSTATE_TMA001_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/registration/msi-imc/transformix/ROI011_PROSTATE_TMA002_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:23<00:00,  1.66s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/preprocessing/imc/ROI011_PROSTATE_TMA002_core.ome.tiff...
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Finished ROI011_PROSTATE_TMA002_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/registration/msi-imc/transformix/ROI011_PROSTATE_TMA002_result.nii...
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Finished ROI011_PROSTATE_TMA002_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/registration/msi-imc/transformix/ROI011_PROSTATE_TMA002_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/registration/msi-imc/transformix/ROI012_PROSTATE_TMA003_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:46<00:00,  1.69s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/preprocessing/imc/ROI012_PROSTATE_TMA003_core.ome.tiff...
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Finished ROI012_PROSTATE_TMA003_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/registration/msi-imc/transformix/ROI012_PROSTATE_TMA003_result.nii...
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Finished ROI012_PROSTATE_TMA003_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/registration/msi-imc/transformix/ROI012_PROSTATE_TMA003_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/registration/msi-imc/transformix/ROI013_PROSTATE_TMA004_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:15<00:00,  1.73s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/preprocessing/imc/ROI013_PROSTATE_TMA004_core.ome.tiff...
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Finished ROI013_PROSTATE_TMA004_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/registration/msi-imc/transformix/ROI013_PROSTATE_TMA004_result.nii...
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Finished ROI013_PROSTATE_TMA004_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/registration/msi-imc/transformix/ROI013_PROSTATE_TMA004_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/registration/msi-imc/transformix/ROI014_PROSTATE_TMA005_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:40<00:00,  1.77s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/preprocessing/imc/ROI014_PROSTATE_TMA005_core.ome.tiff...
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Finished ROI014_PROSTATE_TMA005_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/registration/msi-imc/transformix/ROI014_PROSTATE_TMA005_result.nii...
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Finished ROI014_PROSTATE_TMA005_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/registration/msi-imc/transformix/ROI014_PROSTATE_TMA005_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/preprocessing/imc/ROI015_PROSTATE_TMA006_core.ome.tiff...
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Finished ROI015_PROSTATE_TMA006_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/registration/msi-imc/transformix/ROI016_PROSTATE_TMA007_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:23<00:00,  1.83s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/preprocessing/imc/ROI016_PROSTATE_TMA007_core.ome.tiff...
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Finished ROI016_PROSTATE_TMA007_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/registration/msi-imc/transformix/ROI016_PROSTATE_TMA007_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/registration/msi-imc/transformix/ROI016_PROSTATE_TMA007_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/registration/msi-imc/transformix/ROI017_PROSTATE_TMA008_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [22:17<00:00,  1.91s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/preprocessing/imc/ROI017_PROSTATE_TMA008_core.ome.tiff...
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Finished ROI017_PROSTATE_TMA008_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/registration/msi-imc/transformix/ROI017_PROSTATE_TMA008_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/registration/msi-imc/transformix/ROI017_PROSTATE_TMA008_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/registration/msi-imc/transformix/ROI018_PROSTATE_TMA009_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:45<00:00,  1.86s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/preprocessing/imc/ROI018_PROSTATE_TMA009_core.ome.tiff...
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Finished ROI018_PROSTATE_TMA009_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/registration/msi-imc/transformix/ROI018_PROSTATE_TMA009_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/registration/msi-imc/transformix/ROI018_PROSTATE_TMA009_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/registration/msi-imc/transformix/ROI019_PROSTATE_Benign_TMA008N_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [22:02<00:00,  1.88s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Creating directories for quantification export
Creating directories for quantification export
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/preprocessing/imc/ROI019_PROSTATE_Benign_TMA008N_core.ome.tiff...
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Finished ROI019_PROSTATE_Benign_TMA008N_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/registration/msi-imc/transformix/ROI019_PROSTATE_Benign_TMA008N_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/registration/msi-imc/transformix/ROI019_PROSTATE_Benign_TMA008N_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/registration/msi-imc/transformix/ROI020_PROSTATE_Benign_TMA011N_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:23<00:00,  1.74s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Creating directories for quantification export
Creating directories for quantification export
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/preprocessing/imc/ROI020_PROSTATE_Benign_TMA011N_core.ome.tiff...
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Finished ROI020_PROSTATE_Benign_TMA011N_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/registration/msi-imc/transformix/ROI020_PROSTATE_Benign_TMA011N_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/registration/msi-imc/transformix/ROI020_PROSTATE_Benign_TMA011N_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/registration/msi-imc/transformix/ROI021_PROSTATE_TMA012_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:23<00:00,  1.83s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/preprocessing/imc/ROI021_PROSTATE_TMA012_core.ome.tiff...
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Finished ROI021_PROSTATE_TMA012_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/registration/msi-imc/transformix/ROI021_PROSTATE_TMA012_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/registration/msi-imc/transformix/ROI021_PROSTATE_TMA012_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/registration/msi-imc/transformix/ROI022_PROSTATE_TMA013_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:21<00:00,  1.83s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/preprocessing/imc/ROI022_PROSTATE_TMA013_core.ome.tiff...
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Finished ROI022_PROSTATE_TMA013_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/registration/msi-imc/transformix/ROI022_PROSTATE_TMA013_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/registration/msi-imc/transformix/ROI022_PROSTATE_TMA013_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/registration/msi-imc/transformix/ROI023_PROSTATE_TMA015_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [23:25<00:00,  2.00s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/preprocessing/imc/ROI023_PROSTATE_TMA015_core.ome.tiff...
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Finished ROI023_PROSTATE_TMA015_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/registration/msi-imc/transformix/ROI023_PROSTATE_TMA015_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/registration/msi-imc/transformix/ROI023_PROSTATE_TMA015_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/registration/msi-imc/transformix/ROI024_PROSTATE_TMA016_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:34<00:00,  1.84s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/preprocessing/imc/ROI024_PROSTATE_TMA016_core.ome.tiff...
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Finished ROI024_PROSTATE_TMA016_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/registration/msi-imc/transformix/ROI024_PROSTATE_TMA016_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/registration/msi-imc/transformix/ROI024_PROSTATE_TMA016_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/registration/msi-imc/transformix/ROI025_PROSTATE_TMA017_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:50<00:00,  1.78s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/preprocessing/imc/ROI025_PROSTATE_TMA017_core.ome.tiff...
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Finished ROI025_PROSTATE_TMA017_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/registration/msi-imc/transformix/ROI025_PROSTATE_TMA017_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/registration/msi-imc/transformix/ROI025_PROSTATE_TMA017_result_gradient_magnitude_25.nii...
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Finished ROI025_PROSTATE_TMA017_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/preprocessing/imc/ROI026_PROSTATE_TMA018_core.ome.tiff...
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Finished ROI026_PROSTATE_TMA018_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/registration/msi-imc/transformix/ROI027_PROSTATE_TMA019_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:26<00:00,  1.75s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/preprocessing/imc/ROI027_PROSTATE_TMA019_core.ome.tiff...
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Finished ROI027_PROSTATE_TMA019_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/registration/msi-imc/transformix/ROI027_PROSTATE_TMA019_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/registration/msi-imc/transformix/ROI027_PROSTATE_TMA019_result_gradient_magnitude_25.nii...
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Finished ROI027_PROSTATE_TMA019_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/registration/msi-imc/transformix/ROI028_PROSTATE_TMA020_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:59<00:00,  1.79s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/preprocessing/imc/ROI028_PROSTATE_TMA020_core.ome.tiff...
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Finished ROI028_PROSTATE_TMA020_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/registration/msi-imc/transformix/ROI028_PROSTATE_TMA020_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/registration/msi-imc/transformix/ROI028_PROSTATE_TMA020_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/registration/msi-imc/transformix/ROI029_PROSTATE_TMA022_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [22:03<00:00,  1.89s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/preprocessing/imc/ROI029_PROSTATE_TMA022_core.ome.tiff...
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Finished ROI029_PROSTATE_TMA022_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/registration/msi-imc/transformix/ROI029_PROSTATE_TMA022_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/registration/msi-imc/transformix/ROI029_PROSTATE_TMA022_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/registration/msi-imc/transformix/ROI030_PROSTATE_TMA023_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [22:13<00:00,  1.90s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/preprocessing/imc/ROI030_PROSTATE_TMA023_core.ome.tiff...
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Finished ROI030_PROSTATE_TMA023_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/registration/msi-imc/transformix/ROI030_PROSTATE_TMA023_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/registration/msi-imc/transformix/ROI030_PROSTATE_TMA023_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/registration/msi-imc/transformix/ROI031_PROSTATE_TMA024_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:49<00:00,  1.69s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/preprocessing/imc/ROI031_PROSTATE_TMA024_core.ome.tiff...
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Finished ROI031_PROSTATE_TMA024_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/registration/msi-imc/transformix/ROI031_PROSTATE_TMA024_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/registration/msi-imc/transformix/ROI031_PROSTATE_TMA024_result_gradient_magnitude_25.nii...
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Finished ROI031_PROSTATE_TMA024_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/registration/msi-imc/transformix/ROI032_PROSTATE_TMA025_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:41<00:00,  1.85s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/preprocessing/imc/ROI032_PROSTATE_TMA025_core.ome.tiff...
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Finished ROI032_PROSTATE_TMA025_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/registration/msi-imc/transformix/ROI032_PROSTATE_TMA025_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/registration/msi-imc/transformix/ROI032_PROSTATE_TMA025_result_gradient_magnitude_25.nii...
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Finished ROI032_PROSTATE_TMA025_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/registration/msi-imc/transformix/ROI033_PROSTATE_TMA026_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [18:44<00:00,  1.60s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/preprocessing/imc/ROI033_PROSTATE_TMA026_core.ome.tiff...
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Finished ROI033_PROSTATE_TMA026_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/registration/msi-imc/transformix/ROI033_PROSTATE_TMA026_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/registration/msi-imc/transformix/ROI033_PROSTATE_TMA026_result_gradient_magnitude_25.nii...
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Finished ROI033_PROSTATE_TMA026_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/preprocessing/imc/ROI034_PROSTATE_TMA027_core.ome.tiff...
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Finished ROI034_PROSTATE_TMA027_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/preprocessing/imc/ROI035_PROSTATE_Benign_TMA027N_core.ome.tiff...
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Finished ROI035_PROSTATE_Benign_TMA027N_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/preprocessing/imc/ROI036_PROSTATE_Benign_TMA028N_core.ome.tiff...
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Finished ROI036_PROSTATE_Benign_TMA028N_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/registration/msi-imc/transformix/ROI037_PROSTATE_TMA028_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:02<00:00,  1.80s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/preprocessing/imc/ROI037_PROSTATE_TMA028_core.ome.tiff...
Finished 0
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Finished ROI037_PROSTATE_TMA028_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/registration/msi-imc/transformix/ROI037_PROSTATE_TMA028_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/registration/msi-imc/transformix/ROI037_PROSTATE_TMA028_result_gradient_magnitude_25.nii...
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Finished ROI037_PROSTATE_TMA028_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/registration/msi-imc/transformix/ROI038_PROSTATE_TMA030_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:48<00:00,  1.69s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/preprocessing/imc/ROI038_PROSTATE_TMA030_core.ome.tiff...
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Finished ROI038_PROSTATE_TMA030_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/registration/msi-imc/transformix/ROI038_PROSTATE_TMA030_result.nii...
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Finished ROI038_PROSTATE_TMA030_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/registration/msi-imc/transformix/ROI038_PROSTATE_TMA030_result_gradient_magnitude_25.nii...
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Finished ROI038_PROSTATE_TMA030_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/preprocessing/imc/ROI039_PROSTATE_TMA031_core.ome.tiff...
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Finished ROI039_PROSTATE_TMA031_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/registration/msi-imc/transformix/ROI040_PROSTATE_TMA032_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [22:18<00:00,  1.91s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/preprocessing/imc/ROI040_PROSTATE_TMA032_core.ome.tiff...
Finished 0
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Finished ROI040_PROSTATE_TMA032_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/registration/msi-imc/transformix/ROI040_PROSTATE_TMA032_result.nii...
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Finished ROI040_PROSTATE_TMA032_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/registration/msi-imc/transformix/ROI040_PROSTATE_TMA032_result_gradient_magnitude_25.nii...
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Finished ROI040_PROSTATE_TMA032_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/preprocessing/imc/ROI041_PROSTATE_TMA033_core.ome.tiff...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/preprocessing/imc/ROI042_PROSTATE_TMA034_core.ome.tiff...
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Finished ROI042_PROSTATE_TMA034_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/registration/msi-imc/transformix/ROI043_PROSTATE_TMA035_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:18<00:00,  1.65s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/preprocessing/imc/ROI043_PROSTATE_TMA035_core.ome.tiff...
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Finished ROI043_PROSTATE_TMA035_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/registration/msi-imc/transformix/ROI043_PROSTATE_TMA035_result.nii...
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Finished ROI043_PROSTATE_TMA035_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/registration/msi-imc/transformix/ROI043_PROSTATE_TMA035_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/preprocessing/imc/ROI044_PROSTATE_TMA036_core.ome.tiff...
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Finished ROI044_PROSTATE_TMA036_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/registration/msi-imc/transformix/ROI045_PROSTATE_TMA038_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [24:46<00:00,  2.12s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/preprocessing/imc/ROI045_PROSTATE_TMA038_core.ome.tiff...
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Finished ROI045_PROSTATE_TMA038_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/registration/msi-imc/transformix/ROI045_PROSTATE_TMA038_result.nii...
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Finished ROI045_PROSTATE_TMA038_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/registration/msi-imc/transformix/ROI045_PROSTATE_TMA038_result_gradient_magnitude_25.nii...
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Finished ROI045_PROSTATE_TMA038_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/preprocessing/imc/ROI046_PROSTATE_TMA039_core.ome.tiff...
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Finished ROI046_PROSTATE_TMA039_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/preprocessing/imc/ROI047_PROSTATE_TMA041_core.ome.tiff...
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Finished ROI047_PROSTATE_TMA041_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/registration/msi-imc/transformix/ROI048_PROSTATE_TMA042_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [18:50<00:00,  1.61s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/preprocessing/imc/ROI048_PROSTATE_TMA042_core.ome.tiff...
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Finished ROI048_PROSTATE_TMA042_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/registration/msi-imc/transformix/ROI048_PROSTATE_TMA042_result.nii...
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Finished ROI048_PROSTATE_TMA042_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/registration/msi-imc/transformix/ROI048_PROSTATE_TMA042_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/registration/msi-imc/transformix/ROI049_PROSTATE_TMA044_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [18:56<00:00,  1.62s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/preprocessing/imc/ROI049_PROSTATE_TMA044_core.ome.tiff...
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Finished ROI049_PROSTATE_TMA044_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/registration/msi-imc/transformix/ROI049_PROSTATE_TMA044_result.nii...
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Finished ROI049_PROSTATE_TMA044_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/registration/msi-imc/transformix/ROI049_PROSTATE_TMA044_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/registration/msi-imc/transformix/ROI050_PROSTATE_TMA045_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [23:09<00:00,  1.98s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/preprocessing/imc/ROI050_PROSTATE_TMA045_core.ome.tiff...
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Finished ROI050_PROSTATE_TMA045_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/registration/msi-imc/transformix/ROI050_PROSTATE_TMA045_result.nii...
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Finished ROI050_PROSTATE_TMA045_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/registration/msi-imc/transformix/ROI050_PROSTATE_TMA045_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/registration/msi-imc/transformix/ROI051_PROSTATE_Benign_TMA043N_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [16:42<00:00,  1.43s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Creating directories for quantification export
Creating directories for quantification export
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/preprocessing/imc/ROI051_PROSTATE_Benign_TMA043N_core.ome.tiff...
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Finished ROI051_PROSTATE_Benign_TMA043N_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/registration/msi-imc/transformix/ROI051_PROSTATE_Benign_TMA043N_result.nii...
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Finished ROI051_PROSTATE_Benign_TMA043N_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/registration/msi-imc/transformix/ROI051_PROSTATE_Benign_TMA043N_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/registration/msi-imc/transformix/ROI052_PROSTATE_Benign_TMA046N_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:43<00:00,  1.69s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Creating directories for quantification export
Creating directories for quantification export
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/preprocessing/imc/ROI052_PROSTATE_Benign_TMA046N_core.ome.tiff...
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Finished ROI052_PROSTATE_Benign_TMA046N_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/registration/msi-imc/transformix/ROI052_PROSTATE_Benign_TMA046N_result.nii...
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Finished ROI052_PROSTATE_Benign_TMA046N_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/registration/msi-imc/transformix/ROI052_PROSTATE_Benign_TMA046N_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/preprocessing/imc/ROI053_PROSTATE_TMA046_core.ome.tiff...
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Finished ROI053_PROSTATE_TMA046_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/registration/msi-imc/transformix/ROI054_PROSTATE_TMA048_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [21:12<00:00,  1.81s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/preprocessing/imc/ROI054_PROSTATE_TMA048_core.ome.tiff...
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Finished ROI054_PROSTATE_TMA048_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/registration/msi-imc/transformix/ROI054_PROSTATE_TMA048_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/registration/msi-imc/transformix/ROI054_PROSTATE_TMA048_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/registration/msi-imc/transformix/ROI055_PROSTATE_TMA049_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [15:24<00:00,  1.32s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/preprocessing/imc/ROI055_PROSTATE_TMA049_core.ome.tiff...
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Finished ROI055_PROSTATE_TMA049_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/registration/msi-imc/transformix/ROI055_PROSTATE_TMA049_result.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/preprocessing/imc/ROI056_PROSTATE_TMA054_core.ome.tiff...
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Finished ROI056_PROSTATE_TMA054_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/preprocessing/imc/ROI057_PROSTATE_TMA055_core.ome.tiff...
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Finished ROI057_PROSTATE_TMA055_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/preprocessing/imc/ROI058_PROSTATE_TMA056_core.ome.tiff...
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Finished ROI058_PROSTATE_TMA056_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/preprocessing/imc/ROI059_PROSTATE_TMA057_core.ome.tiff...
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Finished ROI059_PROSTATE_TMA057_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/preprocessing/imc/ROI060_PROSTATE_TMA059_core.ome.tiff...
Finished 0
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Finished ROI060_PROSTATE_TMA059_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/registration/msi-imc/transformix/ROI061_PROSTATE_TMA060_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:03<00:00,  1.63s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/preprocessing/imc/ROI061_PROSTATE_TMA060_core.ome.tiff...
Finished 0
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Finished 61
Finished ROI061_PROSTATE_TMA060_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/registration/msi-imc/transformix/ROI061_PROSTATE_TMA060_result.nii...
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Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/registration/msi-imc/transformix/ROI061_PROSTATE_TMA060_result_gradient_magnitude_25.nii...
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Finished ROI061_PROSTATE_TMA060_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/registration/msi-imc/transformix/ROI062_PROSTATE_TMA061_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [20:50<00:00,  1.78s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/preprocessing/imc/ROI062_PROSTATE_TMA061_core.ome.tiff...
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Finished ROI062_PROSTATE_TMA061_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/registration/msi-imc/transformix/ROI062_PROSTATE_TMA061_result.nii...
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Finished ROI062_PROSTATE_TMA061_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/registration/msi-imc/transformix/ROI062_PROSTATE_TMA061_result_gradient_magnitude_25.nii...
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Finished ROI062_PROSTATE_TMA061_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/preprocessing/imc/ROI063_PROSTATE_TMA062_core.ome.tiff...
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Finished ROI063_PROSTATE_TMA062_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/registration/msi-imc/transformix/ROI064_PROSTATE_Benign_TMA063N_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [18:16<00:00,  1.56s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Creating directories for quantification export
Creating directories for quantification export
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/preprocessing/imc/ROI064_PROSTATE_Benign_TMA063N_core.ome.tiff...
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Finished ROI064_PROSTATE_Benign_TMA063N_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/registration/msi-imc/transformix/ROI064_PROSTATE_Benign_TMA063N_result.nii...
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Finished ROI064_PROSTATE_Benign_TMA063N_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/registration/msi-imc/transformix/ROI064_PROSTATE_Benign_TMA063N_result_gradient_magnitude_25.nii...
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Finished ROI064_PROSTATE_Benign_TMA063N_result_gradient_magnitude_25
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/preprocessing/imc/ROI065_PROSTATE_Benign_TMA064N_core.ome.tiff...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/preprocessing/imc/ROI066_PROSTATE_TMA064_core.ome.tiff...
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Finished ROI066_PROSTATE_TMA064_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/preprocessing/imc/ROI067_PROSTATE_TMA065_core.ome.tiff...
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Finished ROI067_PROSTATE_TMA065_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/provenance/miaaim-quant-hdiseg-ilastik.sh

INFO:root:Valid path...
INFO:root:Valid file extension...
INFO:root:file name: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/registration/msi-imc/transformix/ROI068_PROSTATE_TMA066_result.nii
INFO:root:Finished parsing nifti
INFO:root:Finished
Computing image gradients: 100%|██████████████████████████████████████████████████████| 702/702 [19:27<00:00,  1.66s/it]

MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/preprocessing/imc/ROI068_PROSTATE_TMA066_core.ome.tiff...
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Finished ROI068_PROSTATE_TMA066_core
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/registration/msi-imc/transformix/ROI068_PROSTATE_TMA066_result.nii...
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Finished ROI068_PROSTATE_TMA066_result
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/registration/msi-imc/transformix/ROI068_PROSTATE_TMA066_result_gradient_magnitude_25.nii...
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QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/preprocessing/imc/ROI069_PROSTATE_TMA067_core.ome.tiff...
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Finished ROI069_PROSTATE_TMA067_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/provenance/miaaim-quant-hdiseg-ilastik.sh
MIAAIM QUANTIFICATION
MIAAIM VERSION 0.0.2
METHOD: HDIquantification
ROOT FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070
PROVENANCE FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/provenance
QC FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/qc/quantification/hdiseg-ilastik



PROCESSING DATA
Quantify: extracting single-cell measurements
Extracting single-cell data for /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/preprocessing/imc/ROI070_PROSTATE_TMA070_core.ome.tiff...
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Finished ROI070_PROSTATE_TMA070_core
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/parameters/miaaim-quant-hdiseg-ilastik.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/provenance/miaaim-quant-hdiseg-ilastik.sh