The included training example no longer works #175
Description
Freshly installed python environment with the latest commit (d604104).
Environment:
Package Version Editable project location
------------------------------ -------------- ----------------------------------------------------------------------------
absl-py 2.3.1
aiobotocore 2.17.0
aiohappyeyeballs 2.6.1
aiohttp 3.13.2
aioitertools 0.13.0
aiosignal 1.4.0
annotated-types 0.7.0
asciitree 0.3.3
asttokens 3.0.1
atomicwrites 1.4.1
attrs 25.4.0
blinker 1.9.0
boto3 1.35.81
botocore 1.35.93
cachetools 6.2.2
cellmap-data 2025.9.9.1720
cellmap-flow 0.1.3
cellmap-segmentation-challenge 0.0.1 /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge
cellpose 4.0.7
certifi 2025.11.12
charset-normalizer 3.4.4
click 8.3.1
cloudpickle 3.1.2
contourpy 1.3.3
cycler 0.12.1
daisy 1.2.2
dask 2025.11.0
decorator 5.2.1
Deprecated 1.3.1
dill 0.4.0
eval-type-backport 0.1.3
executing 2.2.1
fasteners 0.20
fastremap 1.17.7
filelock 3.19.1
fill_voids 2.1.1
flasgger 0.9.7.1
Flask 3.1.2
flask-cors 6.0.1
flexcache 0.3
flexparser 0.4
fonttools 4.60.1
frozenlist 1.8.0
fsspec 2025.9.0
funlib.geometry 0.3.0
funlib.math 0.1
google-apitools 0.5.35
google-auth 2.43.0
grpcio 1.76.0
gunicorn 23.0.0
h5py 3.15.1
httplib2 0.31.0
idna 3.11
imagecodecs 2025.11.11
ImageIO 2.37.2
ipython 9.7.0
ipython_pygments_lexers 1.1.1
itsdangerous 2.2.0
jedi 0.19.2
Jinja2 3.1.6
jmespath 1.0.1
joblib 1.5.2
jsonschema 4.25.1
jsonschema-specifications 2025.9.1
kiwisolver 1.4.9
lazy_loader 0.4
lightning 2.5.6
lightning-utilities 0.15.2
locket 1.0.0
Markdown 3.10
MarkupSafe 3.0.2
marshmallow 4.1.0
matplotlib 3.10.7
matplotlib-inline 0.2.1
mistune 3.1.4
ml_collections 1.1.0
ml_dtypes 0.5.4
mpmath 1.3.0
multidict 6.7.0
natsort 8.4.0
networkx 3.5
neuroglancer 2.41.2
numcodecs 0.15.1
numpy 2.2.6
oauth2client 4.1.3
opencv-python-headless 4.12.0.88
packaging 25.0
pandas 2.3.3
parso 0.8.5
partd 1.4.2
pathlib_abc 0.5.2
pexpect 4.9.0
pillow 11.3.0
Pint 0.25.2
pip 23.2.1
platformdirs 4.5.0
prompt_toolkit 3.0.52
propcache 0.4.1
protobuf 6.33.1
ptyprocess 0.7.0
pure_eval 0.2.3
pyasn1 0.6.1
pyasn1_modules 0.4.2
pydantic 2.12.5
pydantic_core 2.41.5
pydantic-ome-ngff 0.6.0
pydantic-zarr 0.7.0
Pygments 2.19.2
pykdtree 1.4.3
pyparsing 3.2.5
python-dateutil 2.9.0.post0
python-dotenv 1.2.1
pytorch-lightning 2.5.6
pytorch-triton-rocm 3.3.1
pytz 2025.2
PyYAML 6.0.3
referencing 0.37.0
requests 2.32.5
roifile 2025.5.10
rpds-py 0.29.0
rsa 4.9.1
s3fs 2025.9.0
s3transfer 0.10.4
scikit-image 0.25.2
scikit-learn 1.7.2
scipy 1.16.3
segment-anything 1.0
setuptools 70.2.0
six 1.17.0
stack-data 0.6.3
structlog 25.5.0
sympy 1.14.0
tensorboard 2.20.0
tensorboard-data-server 0.7.2
tensorboardX 2.6.4
tensorstore 0.1.79
threadpoolctl 3.6.0
tifffile 2025.10.16
toolz 1.1.0
torch 2.7.1+rocm6.3
torchmetrics 1.8.2
torchvision 0.22.1+rocm6.3
tornado 6.5.2
tqdm 4.67.1
traitlets 5.14.3
typing_extensions 4.15.0
typing-inspection 0.4.2
tzdata 2025.2
universal_pathlib 0.3.6
urllib3 2.5.0
wcwidth 0.2.14
Werkzeug 3.1.3
wrapt 1.17.3
xarray 2025.11.0
xarray-ome-ngff 3.1.1
xarray-tensorstore 0.3.0
yarl 1.22.0
zarr 2.18.4
Full log:
/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/venv/bin/python /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/examples/train_2D.py
Training device: cuda
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/labels/groundtruth/crop423 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/labels/groundtruth/crop452 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop179 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop184 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop230 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop231 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney-3/jrc_mus-kidney-3.zarr/recon-1/labels/groundtruth/crop472 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney-glomerulus-2/jrc_mus-kidney-glomerulus-2.zarr/recon-1/labels/groundtruth/crop421 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop177 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-3/jrc_mus-liver-3.zarr/recon-1/labels/groundtruth/crop473 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop289 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop324 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop336 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop337 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop345 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop346 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop349 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop351 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop386 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop410 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop412 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop413 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop355 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop356 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop357 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop358 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop367 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop387 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_zf-cardiac-1/jrc_zf-cardiac-1.zarr/recon-1/labels/groundtruth/crop378 due to scale mismatch
Skipping /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_zf-cardiac-1/jrc_zf-cardiac-1.zarr/recon-1/labels/groundtruth/crop379 due to scale mismatch
0%| | 0/273 [00:00<?, ?it/s, Found raw data for jrc_hela-2 at /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/em/fibsem-uint8]Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop234
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop236
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop237
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop239
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop243
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop247
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop248
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop252
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop254
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop256
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop257
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/labels/groundtruth/crop292
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop235
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop238
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop240
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop241
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop242
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop245
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop249
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop255
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop258
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop259
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/labels/groundtruth/crop291
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop116
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop117
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop118
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop119
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ctl-id8-1/jrc_ctl-id8-1.zarr/recon-1/labels/groundtruth/crop130
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop120
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop121
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop122
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop123
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop134
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-mb-1a/jrc_fly-mb-1a.zarr/recon-1/labels/groundtruth/crop178
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-1/labels/groundtruth/crop173
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-1/labels/groundtruth/crop174
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-1/labels/groundtruth/crop176
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-1/labels/groundtruth/crop185
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-1/labels/groundtruth/crop78
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_fly-vnc-1/jrc_fly-vnc-1.zarr/recon-1/labels/groundtruth/crop79
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop1
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop113
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop13
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop14
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop15
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop155
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop16
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop18
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop19
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop23
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop28
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop3
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop4
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop54
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop55
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop56
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop57
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop58
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop59
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop6
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop7
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop8
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop9
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop94
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop95
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-2/jrc_hela-2.zarr/recon-1/labels/groundtruth/crop96
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop100
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop101
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop111
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop181
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop27
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop33
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop34
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop50
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop51
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop60
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop61
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop62
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop63
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop64
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop65
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop85
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop86
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_hela-3/jrc_hela-3.zarr/recon-1/labels/groundtruth/crop87
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop107
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop112
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop126
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop180
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop182
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop35
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop36
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop37
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop38
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop43
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop47
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop66
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop67
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop68
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop69
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop70
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop71
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop91
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop92
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_jurkat-1/jrc_jurkat-1.zarr/recon-1/labels/groundtruth/crop93
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop109
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop110
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop31
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop32
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop39
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop40
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop42
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop48
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop49
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop72
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop73
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop74
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop75
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop76
0%| | 0/273 [00:00<?, ?it/s, Found raw data for jrc_mus-liver at /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/em/fibsem-uint8]Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop77
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop88
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop89
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/labels/groundtruth/crop90
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/labels/groundtruth/crop423
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/labels/groundtruth/crop452
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop129
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop140
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop141
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop146
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop147
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop148
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop149
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop156
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop158
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop159
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop160
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop161
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop162
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop163
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop164
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop165
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop166
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop179
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop184
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop230
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop231
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney-3/jrc_mus-kidney-3.zarr/recon-1/labels/groundtruth/crop472
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-kidney-glomerulus-2/jrc_mus-kidney-glomerulus-2.zarr/recon-1/labels/groundtruth/crop421
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop124
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop125
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop131
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop132
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop133
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop135
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop136
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop137
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop138
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop139
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop142
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop143
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop144
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop145
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop150
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop151
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop157
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop171
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop172
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop175
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop177
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop183
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop416
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop417
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-3/jrc_mus-liver-3.zarr/recon-1/labels/groundtruth/crop473
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop320
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop266
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop267
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop268
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop269
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop270
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop272
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop273
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop274
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop275
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop276
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop277
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop278
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop279
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop280
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop289
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop298
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop313
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop319
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop321
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop322
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop323
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop324
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop325
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop326
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop336
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop337
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop345
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop346
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop349
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop351
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop377
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop386
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop410
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop412
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop413
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop333
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop340
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop341
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop342
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop355
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop356
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop357
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop358
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop367
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop368
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop369
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop370
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop376
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-liver-zon-2/jrc_mus-liver-zon-2.zarr/recon-1/labels/groundtruth/crop387
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_mus-nacc-1/jrc_mus-nacc-1.zarr/recon-1/labels/groundtruth/crop115
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop20
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop22
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop25
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop26
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop80
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop81
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop82
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop83
100%|██████████| 273/273 [00:00<00:00, 2827.63it/s, No classes found]
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop84
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop97
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop98
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop99
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop186
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop187
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop188
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop189
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop201
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop202
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop203
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop206
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop208
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop209
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop210
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop211
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop212
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop213
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop216
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop217
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop218
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop219
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop190
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop191
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop192
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop193
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop195
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop196
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop197
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop198
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop199
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop200
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop214
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop220
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop222
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop224
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop225
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop226
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop227
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/labels/groundtruth/crop228
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_zf-cardiac-1/jrc_zf-cardiac-1.zarr/recon-1/labels/groundtruth/crop378
Processing /mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/data/jrc_zf-cardiac-1/jrc_zf-cardiac-1.zarr/recon-1/labels/groundtruth/crop379
Number of datasets: 243
Number of training datasets: 209 (86.01%)
Number of validation datasets: 34 (13.99%)
CSV written to datasplit.csv
Training datasets: 100%|██████████| 209/209 [00:00<00:00, 316.87it/s]
Validation datasets: 100%|██████████| 34/34 [00:00<00:00, 281.74it/s]
Training datasets: 100%|██████████| 209/209 [00:00<00:00, 363.02it/s]
Validation datasets: 100%|██████████| 34/34 [00:00<00:00, 388.20it/s]
100%|██████████| 178/178 [00:00<00:00, 3200.00it/s]
Training 2d_unet for 1000 epochs, starting at epoch 1, iteration 0...
Training: 0%| | 0/1000 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/image.py", line 250, in array
return self._array
^^^^^^^^^^^
AttributeError: 'CellMapImage' object has no attribute '_array'. Did you mean: 'array'?
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/examples/train_2D.py", line 80, in <module>
train(__file__)
~~~~~^^^^^^^^^^
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-segmentation-challenge/src/cellmap_segmentation_challenge/train.py", line 367, in train
batch = next(loader)
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/dataloader.py", line 234, in _create_iterator
batch_data = [self.dataset[idx] for idx in batch_indices]
~~~~~~~~~~~~^^^^^
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/venv/lib/python3.13/site-packages/torch/utils/data/dataset.py", line 346, in __getitem__
return self.datasets[dataset_idx][sample_idx]
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/dataset.py", line 639, in __getitem__
array_name, array = future.result()
~~~~~~~~~~~~~^^
File "/usr/lib/python3.13/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
~~~~~~~~~~~~~~~~~^^
File "/usr/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/usr/lib/python3.13/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/dataset.py", line 532, in get_input_array
array = self.input_sources[array_name][center] # type: ignore
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/image.py", line 124, in __getitem__
data = self.apply_spatial_transforms(coords)
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/image.py", line 472, in apply_spatial_transforms
data = self.return_data(coords)
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/image.py", line 514, in return_data
data = self.array.interp(
^^^^^^^^^^
File "/mnt/2878EBCCAED823C6/PycharmProjects/cellmap/cellmap-data/src/cellmap_data/image.py", line 262, in array
spec = xt._zarr_spec_from_path(self.array_path)
TypeError: _zarr_spec_from_path() missing 1 required positional argument: 'zarr_format'