Training Ilastik

• Generates and Exports Training Crops

# Ilastik pixel classification preparation
# import custom modules
from miaaim.probs.ilastik.ilastik import Ilastik

# import external modules
from pathlib import Path
import pandas as pd
import os

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

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

# set path to project folder
project_folder = Path("/opt/miaaim-20220912-TMA4")
# set path to data folder
data_folder = project_folder.joinpath("data")

# get image preprocessing channels to use as a list of indices
prep_channels = pd.read_csv(Path(data_folder).joinpath("imc-preprocessing-markers.csv"))
prep_channels = [int(prep_channels.Page.values[i]) for i in range(len(prep_channels.Page.values))]

# get list of all images in the data folder (all used for training)
core_folders =[data_folder.joinpath(c) for c in os.listdir(data_folder) if data_folder.joinpath(c).is_dir()]

# check to make sure we have the core folders for only prostate samples
core_folders = [c for c in core_folders if "PROSTATE" in c.name]
core_folders

[PosixPath('/opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067'),
 PosixPath('/opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070')]

# iterate over cores in the image list and prepare training crops
for c in core_folders:
    # get the stem of image (folder name)
    name = "preprocessing/imc/" + f"{c.stem}"+ "_core.ome.tiff"
    # set root folder
    root_folder = data_folder.joinpath(c.stem)
    # set input image
    input_image = c.joinpath(name)

    # create Ilastik object
    IL = Ilastik(
        root_folder=root_folder,
        input_image=input_image,
        name=None,
        executable=None,
        qc=True,
        resume=False
        )

    # prepare training
    IL.PrepareTraining(
        input_image=None,
        channelIDs=prep_channels,
        nonzero_fraction=0.05
        )

MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI010_PROSTATE_TMA001_core.ome...
Finished exporting image
Export ROI010_PROSTATE_TMA001_core_crop0.hdf5...
Finished exporting ROI010_PROSTATE_TMA001_core_crop0.hdf5
Export ROI010_PROSTATE_TMA001_core_crop1.hdf5...
Finished exporting ROI010_PROSTATE_TMA001_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI010_PROSTATE_TMA001/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI011_PROSTATE_TMA002_core.ome...
Finished exporting image
Export ROI011_PROSTATE_TMA002_core_crop0.hdf5...
Finished exporting ROI011_PROSTATE_TMA002_core_crop0.hdf5
Export ROI011_PROSTATE_TMA002_core_crop1.hdf5...
Finished exporting ROI011_PROSTATE_TMA002_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI011_PROSTATE_TMA002/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI012_PROSTATE_TMA003_core.ome...
Finished exporting image
Export ROI012_PROSTATE_TMA003_core_crop0.hdf5...
Finished exporting ROI012_PROSTATE_TMA003_core_crop0.hdf5
Export ROI012_PROSTATE_TMA003_core_crop1.hdf5...
Finished exporting ROI012_PROSTATE_TMA003_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI012_PROSTATE_TMA003/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI013_PROSTATE_TMA004_core.ome...
Finished exporting image
Export ROI013_PROSTATE_TMA004_core_crop0.hdf5...
Finished exporting ROI013_PROSTATE_TMA004_core_crop0.hdf5
Export ROI013_PROSTATE_TMA004_core_crop1.hdf5...
Finished exporting ROI013_PROSTATE_TMA004_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI013_PROSTATE_TMA004/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI014_PROSTATE_TMA005_core.ome...
Finished exporting image
Export ROI014_PROSTATE_TMA005_core_crop0.hdf5...
Finished exporting ROI014_PROSTATE_TMA005_core_crop0.hdf5
Export ROI014_PROSTATE_TMA005_core_crop1.hdf5...
Finished exporting ROI014_PROSTATE_TMA005_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI014_PROSTATE_TMA005/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI015_PROSTATE_TMA006_core.ome...
Finished exporting image
Export ROI015_PROSTATE_TMA006_core_crop0.hdf5...
Finished exporting ROI015_PROSTATE_TMA006_core_crop0.hdf5
Export ROI015_PROSTATE_TMA006_core_crop1.hdf5...
Finished exporting ROI015_PROSTATE_TMA006_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI015_PROSTATE_TMA006/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI016_PROSTATE_TMA007_core.ome...
Finished exporting image
Export ROI016_PROSTATE_TMA007_core_crop0.hdf5...
Finished exporting ROI016_PROSTATE_TMA007_core_crop0.hdf5
Export ROI016_PROSTATE_TMA007_core_crop1.hdf5...
Finished exporting ROI016_PROSTATE_TMA007_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI016_PROSTATE_TMA007/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI017_PROSTATE_TMA008_core.ome...
Finished exporting image
Export ROI017_PROSTATE_TMA008_core_crop0.hdf5...
Finished exporting ROI017_PROSTATE_TMA008_core_crop0.hdf5
Export ROI017_PROSTATE_TMA008_core_crop1.hdf5...
Finished exporting ROI017_PROSTATE_TMA008_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI017_PROSTATE_TMA008/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI018_PROSTATE_TMA009_core.ome...
Finished exporting image
Export ROI018_PROSTATE_TMA009_core_crop0.hdf5...
Finished exporting ROI018_PROSTATE_TMA009_core_crop0.hdf5
Export ROI018_PROSTATE_TMA009_core_crop1.hdf5...
Finished exporting ROI018_PROSTATE_TMA009_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI018_PROSTATE_TMA009/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI019_PROSTATE_Benign_TMA008N_core.ome...
Finished exporting image
Export ROI019_PROSTATE_Benign_TMA008N_core_crop0.hdf5...
Finished exporting ROI019_PROSTATE_Benign_TMA008N_core_crop0.hdf5
Export ROI019_PROSTATE_Benign_TMA008N_core_crop1.hdf5...
Finished exporting ROI019_PROSTATE_Benign_TMA008N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI019_PROSTATE_Benign_TMA008N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI020_PROSTATE_Benign_TMA011N_core.ome...
Finished exporting image
Export ROI020_PROSTATE_Benign_TMA011N_core_crop0.hdf5...
Finished exporting ROI020_PROSTATE_Benign_TMA011N_core_crop0.hdf5
Export ROI020_PROSTATE_Benign_TMA011N_core_crop1.hdf5...
Finished exporting ROI020_PROSTATE_Benign_TMA011N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI020_PROSTATE_Benign_TMA011N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI021_PROSTATE_TMA012_core.ome...
Finished exporting image
Export ROI021_PROSTATE_TMA012_core_crop0.hdf5...
Finished exporting ROI021_PROSTATE_TMA012_core_crop0.hdf5
Export ROI021_PROSTATE_TMA012_core_crop1.hdf5...
Finished exporting ROI021_PROSTATE_TMA012_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI021_PROSTATE_TMA012/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI022_PROSTATE_TMA013_core.ome...
Finished exporting image
Export ROI022_PROSTATE_TMA013_core_crop0.hdf5...
Finished exporting ROI022_PROSTATE_TMA013_core_crop0.hdf5
Export ROI022_PROSTATE_TMA013_core_crop1.hdf5...
Finished exporting ROI022_PROSTATE_TMA013_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI022_PROSTATE_TMA013/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI023_PROSTATE_TMA015_core.ome...
Finished exporting image
Export ROI023_PROSTATE_TMA015_core_crop0.hdf5...
Finished exporting ROI023_PROSTATE_TMA015_core_crop0.hdf5
Export ROI023_PROSTATE_TMA015_core_crop1.hdf5...
Finished exporting ROI023_PROSTATE_TMA015_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI023_PROSTATE_TMA015/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI024_PROSTATE_TMA016_core.ome...
Finished exporting image
Export ROI024_PROSTATE_TMA016_core_crop0.hdf5...
Finished exporting ROI024_PROSTATE_TMA016_core_crop0.hdf5
Export ROI024_PROSTATE_TMA016_core_crop1.hdf5...
Finished exporting ROI024_PROSTATE_TMA016_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI024_PROSTATE_TMA016/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI025_PROSTATE_TMA017_core.ome...
Finished exporting image
Export ROI025_PROSTATE_TMA017_core_crop0.hdf5...
Finished exporting ROI025_PROSTATE_TMA017_core_crop0.hdf5
Export ROI025_PROSTATE_TMA017_core_crop1.hdf5...
Finished exporting ROI025_PROSTATE_TMA017_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI025_PROSTATE_TMA017/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI026_PROSTATE_TMA018_core.ome...
Finished exporting image
Export ROI026_PROSTATE_TMA018_core_crop0.hdf5...
Finished exporting ROI026_PROSTATE_TMA018_core_crop0.hdf5
Export ROI026_PROSTATE_TMA018_core_crop1.hdf5...
Finished exporting ROI026_PROSTATE_TMA018_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI026_PROSTATE_TMA018/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI027_PROSTATE_TMA019_core.ome...
Finished exporting image
Export ROI027_PROSTATE_TMA019_core_crop0.hdf5...
Finished exporting ROI027_PROSTATE_TMA019_core_crop0.hdf5
Export ROI027_PROSTATE_TMA019_core_crop1.hdf5...
Finished exporting ROI027_PROSTATE_TMA019_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI027_PROSTATE_TMA019/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI028_PROSTATE_TMA020_core.ome...
Finished exporting image
Export ROI028_PROSTATE_TMA020_core_crop0.hdf5...
Finished exporting ROI028_PROSTATE_TMA020_core_crop0.hdf5
Export ROI028_PROSTATE_TMA020_core_crop1.hdf5...
Finished exporting ROI028_PROSTATE_TMA020_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI028_PROSTATE_TMA020/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI029_PROSTATE_TMA022_core.ome...
Finished exporting image
Export ROI029_PROSTATE_TMA022_core_crop0.hdf5...
Finished exporting ROI029_PROSTATE_TMA022_core_crop0.hdf5
Export ROI029_PROSTATE_TMA022_core_crop1.hdf5...
Finished exporting ROI029_PROSTATE_TMA022_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI029_PROSTATE_TMA022/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI030_PROSTATE_TMA023_core.ome...
Finished exporting image
Export ROI030_PROSTATE_TMA023_core_crop0.hdf5...
Finished exporting ROI030_PROSTATE_TMA023_core_crop0.hdf5
Export ROI030_PROSTATE_TMA023_core_crop1.hdf5...
Finished exporting ROI030_PROSTATE_TMA023_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI030_PROSTATE_TMA023/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI031_PROSTATE_TMA024_core.ome...
Finished exporting image
Export ROI031_PROSTATE_TMA024_core_crop0.hdf5...
Finished exporting ROI031_PROSTATE_TMA024_core_crop0.hdf5
Export ROI031_PROSTATE_TMA024_core_crop1.hdf5...
Finished exporting ROI031_PROSTATE_TMA024_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI031_PROSTATE_TMA024/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI032_PROSTATE_TMA025_core.ome...
Finished exporting image
Export ROI032_PROSTATE_TMA025_core_crop0.hdf5...
Finished exporting ROI032_PROSTATE_TMA025_core_crop0.hdf5
Export ROI032_PROSTATE_TMA025_core_crop1.hdf5...
Finished exporting ROI032_PROSTATE_TMA025_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI032_PROSTATE_TMA025/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI033_PROSTATE_TMA026_core.ome...
Finished exporting image
Export ROI033_PROSTATE_TMA026_core_crop0.hdf5...
Finished exporting ROI033_PROSTATE_TMA026_core_crop0.hdf5
Export ROI033_PROSTATE_TMA026_core_crop1.hdf5...
Finished exporting ROI033_PROSTATE_TMA026_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI033_PROSTATE_TMA026/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI034_PROSTATE_TMA027_core.ome...
Finished exporting image
Export ROI034_PROSTATE_TMA027_core_crop0.hdf5...
Finished exporting ROI034_PROSTATE_TMA027_core_crop0.hdf5
Export ROI034_PROSTATE_TMA027_core_crop1.hdf5...
Finished exporting ROI034_PROSTATE_TMA027_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI034_PROSTATE_TMA027/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI035_PROSTATE_Benign_TMA027N_core.ome...
Finished exporting image
Export ROI035_PROSTATE_Benign_TMA027N_core_crop0.hdf5...
Finished exporting ROI035_PROSTATE_Benign_TMA027N_core_crop0.hdf5
Export ROI035_PROSTATE_Benign_TMA027N_core_crop1.hdf5...
Finished exporting ROI035_PROSTATE_Benign_TMA027N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI035_PROSTATE_Benign_TMA027N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI036_PROSTATE_Benign_TMA028N_core.ome...
Finished exporting image
Export ROI036_PROSTATE_Benign_TMA028N_core_crop0.hdf5...
Finished exporting ROI036_PROSTATE_Benign_TMA028N_core_crop0.hdf5
Export ROI036_PROSTATE_Benign_TMA028N_core_crop1.hdf5...
Finished exporting ROI036_PROSTATE_Benign_TMA028N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI036_PROSTATE_Benign_TMA028N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI037_PROSTATE_TMA028_core.ome...
Finished exporting image
Export ROI037_PROSTATE_TMA028_core_crop0.hdf5...
Finished exporting ROI037_PROSTATE_TMA028_core_crop0.hdf5
Export ROI037_PROSTATE_TMA028_core_crop1.hdf5...
Finished exporting ROI037_PROSTATE_TMA028_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI037_PROSTATE_TMA028/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI038_PROSTATE_TMA030_core.ome...
Finished exporting image
Export ROI038_PROSTATE_TMA030_core_crop0.hdf5...
Finished exporting ROI038_PROSTATE_TMA030_core_crop0.hdf5
Export ROI038_PROSTATE_TMA030_core_crop1.hdf5...
Finished exporting ROI038_PROSTATE_TMA030_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI038_PROSTATE_TMA030/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI039_PROSTATE_TMA031_core.ome...
Finished exporting image
Export ROI039_PROSTATE_TMA031_core_crop0.hdf5...
Finished exporting ROI039_PROSTATE_TMA031_core_crop0.hdf5
Export ROI039_PROSTATE_TMA031_core_crop1.hdf5...
Finished exporting ROI039_PROSTATE_TMA031_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI039_PROSTATE_TMA031/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI040_PROSTATE_TMA032_core.ome...
Finished exporting image
Export ROI040_PROSTATE_TMA032_core_crop0.hdf5...
Finished exporting ROI040_PROSTATE_TMA032_core_crop0.hdf5
Export ROI040_PROSTATE_TMA032_core_crop1.hdf5...
Finished exporting ROI040_PROSTATE_TMA032_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI040_PROSTATE_TMA032/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI041_PROSTATE_TMA033_core.ome...
Finished exporting image
Export ROI041_PROSTATE_TMA033_core_crop0.hdf5...
Finished exporting ROI041_PROSTATE_TMA033_core_crop0.hdf5
Export ROI041_PROSTATE_TMA033_core_crop1.hdf5...
Finished exporting ROI041_PROSTATE_TMA033_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI041_PROSTATE_TMA033/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI042_PROSTATE_TMA034_core.ome...
Finished exporting image
Export ROI042_PROSTATE_TMA034_core_crop0.hdf5...
Finished exporting ROI042_PROSTATE_TMA034_core_crop0.hdf5
Export ROI042_PROSTATE_TMA034_core_crop1.hdf5...
Finished exporting ROI042_PROSTATE_TMA034_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI042_PROSTATE_TMA034/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI043_PROSTATE_TMA035_core.ome...
Finished exporting image
Export ROI043_PROSTATE_TMA035_core_crop0.hdf5...
Finished exporting ROI043_PROSTATE_TMA035_core_crop0.hdf5
Export ROI043_PROSTATE_TMA035_core_crop1.hdf5...
Finished exporting ROI043_PROSTATE_TMA035_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI043_PROSTATE_TMA035/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI044_PROSTATE_TMA036_core.ome...
Finished exporting image
Export ROI044_PROSTATE_TMA036_core_crop0.hdf5...
Finished exporting ROI044_PROSTATE_TMA036_core_crop0.hdf5
Export ROI044_PROSTATE_TMA036_core_crop1.hdf5...
Finished exporting ROI044_PROSTATE_TMA036_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI044_PROSTATE_TMA036/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI045_PROSTATE_TMA038_core.ome...
Finished exporting image
Export ROI045_PROSTATE_TMA038_core_crop0.hdf5...
Finished exporting ROI045_PROSTATE_TMA038_core_crop0.hdf5
Export ROI045_PROSTATE_TMA038_core_crop1.hdf5...
Finished exporting ROI045_PROSTATE_TMA038_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI045_PROSTATE_TMA038/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI046_PROSTATE_TMA039_core.ome...
Finished exporting image
Export ROI046_PROSTATE_TMA039_core_crop0.hdf5...
Finished exporting ROI046_PROSTATE_TMA039_core_crop0.hdf5
Export ROI046_PROSTATE_TMA039_core_crop1.hdf5...
Finished exporting ROI046_PROSTATE_TMA039_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI046_PROSTATE_TMA039/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI047_PROSTATE_TMA041_core.ome...
Finished exporting image
Export ROI047_PROSTATE_TMA041_core_crop0.hdf5...
Finished exporting ROI047_PROSTATE_TMA041_core_crop0.hdf5
Export ROI047_PROSTATE_TMA041_core_crop1.hdf5...
Finished exporting ROI047_PROSTATE_TMA041_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI047_PROSTATE_TMA041/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI048_PROSTATE_TMA042_core.ome...
Finished exporting image
Export ROI048_PROSTATE_TMA042_core_crop0.hdf5...
Finished exporting ROI048_PROSTATE_TMA042_core_crop0.hdf5
Export ROI048_PROSTATE_TMA042_core_crop1.hdf5...
Finished exporting ROI048_PROSTATE_TMA042_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI048_PROSTATE_TMA042/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI049_PROSTATE_TMA044_core.ome...
Finished exporting image
Export ROI049_PROSTATE_TMA044_core_crop0.hdf5...
Finished exporting ROI049_PROSTATE_TMA044_core_crop0.hdf5
Export ROI049_PROSTATE_TMA044_core_crop1.hdf5...
Finished exporting ROI049_PROSTATE_TMA044_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI049_PROSTATE_TMA044/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI050_PROSTATE_TMA045_core.ome...
Finished exporting image
Export ROI050_PROSTATE_TMA045_core_crop0.hdf5...
Finished exporting ROI050_PROSTATE_TMA045_core_crop0.hdf5
Export ROI050_PROSTATE_TMA045_core_crop1.hdf5...
Finished exporting ROI050_PROSTATE_TMA045_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI050_PROSTATE_TMA045/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI051_PROSTATE_Benign_TMA043N_core.ome...
Finished exporting image
Export ROI051_PROSTATE_Benign_TMA043N_core_crop0.hdf5...
Finished exporting ROI051_PROSTATE_Benign_TMA043N_core_crop0.hdf5
Export ROI051_PROSTATE_Benign_TMA043N_core_crop1.hdf5...
Finished exporting ROI051_PROSTATE_Benign_TMA043N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI051_PROSTATE_Benign_TMA043N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI052_PROSTATE_Benign_TMA046N_core.ome...
Finished exporting image
Export ROI052_PROSTATE_Benign_TMA046N_core_crop0.hdf5...
Finished exporting ROI052_PROSTATE_Benign_TMA046N_core_crop0.hdf5
Export ROI052_PROSTATE_Benign_TMA046N_core_crop1.hdf5...
Finished exporting ROI052_PROSTATE_Benign_TMA046N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI052_PROSTATE_Benign_TMA046N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI053_PROSTATE_TMA046_core.ome...
Finished exporting image
Export ROI053_PROSTATE_TMA046_core_crop0.hdf5...
Finished exporting ROI053_PROSTATE_TMA046_core_crop0.hdf5
Export ROI053_PROSTATE_TMA046_core_crop1.hdf5...
Finished exporting ROI053_PROSTATE_TMA046_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI053_PROSTATE_TMA046/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI054_PROSTATE_TMA048_core.ome...
Finished exporting image
Export ROI054_PROSTATE_TMA048_core_crop0.hdf5...
Finished exporting ROI054_PROSTATE_TMA048_core_crop0.hdf5
Export ROI054_PROSTATE_TMA048_core_crop1.hdf5...
Finished exporting ROI054_PROSTATE_TMA048_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI054_PROSTATE_TMA048/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI055_PROSTATE_TMA049_core.ome...
Finished exporting image
Export ROI055_PROSTATE_TMA049_core_crop0.hdf5...
Finished exporting ROI055_PROSTATE_TMA049_core_crop0.hdf5
Export ROI055_PROSTATE_TMA049_core_crop1.hdf5...
Finished exporting ROI055_PROSTATE_TMA049_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI055_PROSTATE_TMA049/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI056_PROSTATE_TMA054_core.ome...
Finished exporting image
Export ROI056_PROSTATE_TMA054_core_crop0.hdf5...
Finished exporting ROI056_PROSTATE_TMA054_core_crop0.hdf5
Export ROI056_PROSTATE_TMA054_core_crop1.hdf5...
Finished exporting ROI056_PROSTATE_TMA054_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI056_PROSTATE_TMA054/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI057_PROSTATE_TMA055_core.ome...
Finished exporting image
Export ROI057_PROSTATE_TMA055_core_crop0.hdf5...
Finished exporting ROI057_PROSTATE_TMA055_core_crop0.hdf5
Export ROI057_PROSTATE_TMA055_core_crop1.hdf5...
Finished exporting ROI057_PROSTATE_TMA055_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI057_PROSTATE_TMA055/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI058_PROSTATE_TMA056_core.ome...
Finished exporting image
Export ROI058_PROSTATE_TMA056_core_crop0.hdf5...
Finished exporting ROI058_PROSTATE_TMA056_core_crop0.hdf5
Export ROI058_PROSTATE_TMA056_core_crop1.hdf5...
Finished exporting ROI058_PROSTATE_TMA056_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI058_PROSTATE_TMA056/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI059_PROSTATE_TMA057_core.ome...
Finished exporting image
Export ROI059_PROSTATE_TMA057_core_crop0.hdf5...
Finished exporting ROI059_PROSTATE_TMA057_core_crop0.hdf5
Export ROI059_PROSTATE_TMA057_core_crop1.hdf5...
Finished exporting ROI059_PROSTATE_TMA057_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI059_PROSTATE_TMA057/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI060_PROSTATE_TMA059_core.ome...
Finished exporting image
Export ROI060_PROSTATE_TMA059_core_crop0.hdf5...
Finished exporting ROI060_PROSTATE_TMA059_core_crop0.hdf5
Export ROI060_PROSTATE_TMA059_core_crop1.hdf5...
Finished exporting ROI060_PROSTATE_TMA059_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI060_PROSTATE_TMA059/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI061_PROSTATE_TMA060_core.ome...
Finished exporting image
Export ROI061_PROSTATE_TMA060_core_crop0.hdf5...
Finished exporting ROI061_PROSTATE_TMA060_core_crop0.hdf5
Export ROI061_PROSTATE_TMA060_core_crop1.hdf5...
Finished exporting ROI061_PROSTATE_TMA060_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI061_PROSTATE_TMA060/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI062_PROSTATE_TMA061_core.ome...
Finished exporting image
Export ROI062_PROSTATE_TMA061_core_crop0.hdf5...
Finished exporting ROI062_PROSTATE_TMA061_core_crop0.hdf5
Export ROI062_PROSTATE_TMA061_core_crop1.hdf5...
Finished exporting ROI062_PROSTATE_TMA061_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI062_PROSTATE_TMA061/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI063_PROSTATE_TMA062_core.ome...
Finished exporting image
Export ROI063_PROSTATE_TMA062_core_crop0.hdf5...
Finished exporting ROI063_PROSTATE_TMA062_core_crop0.hdf5
Export ROI063_PROSTATE_TMA062_core_crop1.hdf5...
Finished exporting ROI063_PROSTATE_TMA062_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI063_PROSTATE_TMA062/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI064_PROSTATE_Benign_TMA063N_core.ome...
Finished exporting image
Export ROI064_PROSTATE_Benign_TMA063N_core_crop0.hdf5...
Finished exporting ROI064_PROSTATE_Benign_TMA063N_core_crop0.hdf5
Export ROI064_PROSTATE_Benign_TMA063N_core_crop1.hdf5...
Finished exporting ROI064_PROSTATE_Benign_TMA063N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI064_PROSTATE_Benign_TMA063N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI065_PROSTATE_Benign_TMA064N_core.ome...
Finished exporting image
Export ROI065_PROSTATE_Benign_TMA064N_core_crop0.hdf5...
Finished exporting ROI065_PROSTATE_Benign_TMA064N_core_crop0.hdf5
Export ROI065_PROSTATE_Benign_TMA064N_core_crop1.hdf5...
Finished exporting ROI065_PROSTATE_Benign_TMA064N_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI065_PROSTATE_Benign_TMA064N/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI066_PROSTATE_TMA064_core.ome...
Finished exporting image
Export ROI066_PROSTATE_TMA064_core_crop0.hdf5...
Finished exporting ROI066_PROSTATE_TMA064_core_crop0.hdf5
Export ROI066_PROSTATE_TMA064_core_crop1.hdf5...
Finished exporting ROI066_PROSTATE_TMA064_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI066_PROSTATE_TMA064/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI067_PROSTATE_TMA065_core.ome...
Finished exporting image
Export ROI067_PROSTATE_TMA065_core_crop0.hdf5...
Finished exporting ROI067_PROSTATE_TMA065_core_crop0.hdf5
Export ROI067_PROSTATE_TMA065_core_crop1.hdf5...
Finished exporting ROI067_PROSTATE_TMA065_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI067_PROSTATE_TMA065/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI068_PROSTATE_TMA066_core.ome...
Finished exporting image
Export ROI068_PROSTATE_TMA066_core_crop0.hdf5...
Finished exporting ROI068_PROSTATE_TMA066_core_crop0.hdf5
Export ROI068_PROSTATE_TMA066_core_crop1.hdf5...
Finished exporting ROI068_PROSTATE_TMA066_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI068_PROSTATE_TMA066/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI069_PROSTATE_TMA067_core.ome...
Finished exporting image
Export ROI069_PROSTATE_TMA067_core_crop0.hdf5...
Finished exporting ROI069_PROSTATE_TMA067_core_crop0.hdf5
Export ROI069_PROSTATE_TMA067_core_crop1.hdf5...
Finished exporting ROI069_PROSTATE_TMA067_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI069_PROSTATE_TMA067/docs/provenance/miaaim-prob-ilastik-imc.sh
MIAAIM PROBABILITIES
MIAAIM VERSION 0.0.2
METHOD: Ilastik
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/probabilities/imc/ilastik



PROCESSING DATA
TRAINING DATA FOLDER: /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/probabilities/imc/ilastik-training
PREPARING DATA FOR PIXEL CLASSIFICATION
Reading ROI070_PROSTATE_TMA070_core.ome...
Finished exporting image
Export ROI070_PROSTATE_TMA070_core_crop0.hdf5...
Finished exporting ROI070_PROSTATE_TMA070_core_crop0.hdf5
Export ROI070_PROSTATE_TMA070_core_crop1.hdf5...
Finished exporting ROI070_PROSTATE_TMA070_core_crop1.hdf5
QC: extracting quality control information
Exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/parameters/miaaim-prob-ilastik-imc.yaml
Exporting /opt/miaaim-20220912-TMA4/data/ROI070_PROSTATE_TMA070/docs/provenance/miaaim-prob-ilastik-imc.sh