Nuclear Mask Dilation: follow up to issue #1009

[marsdenl]

Hey there,
In the context of segmentation of MERSCOPE data using a trained Cellpose 2.0 model with Vizgen's VPT plugin, I finally got around to trying the nuclear expansion method. I downloaded the fork (https://github.com/carsen-stringer/vizgen-postprocessing) into a venv and ran essentially the exact same code that I used prior to run my cellpose 2.0 model via VPT:

vpt --verbose run-segmentation ^
--segmentation-algorithm "cellpose2_CP_20241028_115219_v4-expanded.json" ^
--input-images "images\mosaic_(?P[\w|-]+)_z(?P[0-9]+).tif" ^
--input-micron-to-mosaic "images\micron_to_mosaic_pixel_transform.csv" ^
--output "analysis_outputs_customv5" ^
--tile-size 2400 ^
--tile-overlap 200

My only modification was in the .json file where I added a "dilation" = 2.0 line under segmentation parameters:
cellpose2_CP_20241028_115219_v4_expanded.json

When I ran the code, I got the following error:
File "C:\Users\marsdenl~.venv\vpt-fork-env\lib\site-packages\vpt\prepare_segmentation\validate.py", line 14, in validate_regex_and_alg_match
raise ValueError(f'Z planes from algorithm specification {alg_info.z_layers} do not match '
ValueError: Z planes from algorithm specification {1, 3, 5} do not match z planes extracted from regular expression set()

This is the same regex recommended by VPT, I have used it in the non-forked version of VPT and it worked at the time. I also get the same error when I remove the dilation parameter from the .json file. I do not get the error with the same code and .json (without the dilation parameter) but in my other VPT venv. Do you have any ideas why that might be happening? I have not changed my image names, when I try the regex independently of the forked function, it seems fine. Thank you in advance for your help!

Packages in venv:

absl-py==2.1.0
affine==2.4.0
aiobotocore==1.4.2
aiohappyeyeballs==2.4.3
aiohttp==3.11.7
aioitertools==0.12.0
aiosignal==1.3.1
astunparse==1.6.3
async-timeout==5.0.1
attrs==24.2.0
boto3==1.17.0
botocore==1.20.106
cachetools==5.5.0
cellpose==1.0.2
certifi==2024.8.30
cffi==1.17.1
charset-normalizer==3.4.0
click==8.1.7
click-plugins==1.1.1
cligj==0.7.2
cloudpickle==3.1.0
colorama==0.4.6
contourpy==1.2.1
csbdeep==0.8.1
cycler==0.12.1
dask==2022.9.0
decorator==5.1.1
distributed==2022.9.0
fastremap==1.15.0
filelock==3.16.1
fiona==1.10.1
flatbuffers==1.12
fonttools==4.55.0
frozenlist==1.5.0
fsspec==2021.10.0
gast==0.4.0
gcsfs==2021.10.0
geojson==2.5.0
geopandas==0.12.1
google-auth==2.36.0
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio==1.68.0
h5py==3.7.0
idna==3.10
imageio==2.36.0
Jinja2==3.1.4
jmespath==0.10.0
keras==2.9.0
Keras-Preprocessing==1.1.2
kiwisolver==1.4.7
libclang==18.1.1
llvmlite==0.43.0
locket==1.0.0
Markdown==3.7
MarkupSafe==3.0.2
matplotlib==3.8.4
mpmath==1.3.0
msgpack==1.1.0
multidict==6.1.0
natsort==8.4.0
networkx==3.4.2
numba==0.60.0
numpy==1.22.4
oauthlib==3.2.2
opencv-python-headless==4.6.0.66
opt_einsum==3.4.0
packaging==24.2
pandas==1.4.3
partd==1.4.2
pillow==11.0.0
propcache==0.2.0
protobuf==3.19.6
psutil==6.1.0
pyarrow==8.0.0
pyasn1==0.6.1
pyasn1_modules==0.4.1
pyclustering==0.10.1.2
pycparser==2.22
pyparsing==3.2.0
pyproj==3.7.0
python-dateutil==2.9.0.post0
python-dotenv==0.20.0
pytz==2024.2
pyvips==2.2.1
PyWavelets==1.6.0
PyYAML==6.0.2
rasterio==1.3.0
requests==2.32.3
requests-oauthlib==2.0.0
rsa==4.9
s3fs==2021.10.0
s3transfer==0.3.7
scikit-image==0.19.3
scipy==1.8.1
shapely==2.0.0
six==1.16.0
snuggs==1.4.7
sortedcontainers==2.4.0
stardist==0.8.3
sympy==1.13.1
tblib==3.0.0
tensorboard==2.9.1
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow==2.9.1
tensorflow-estimator==2.9.0
tensorflow-io-gcs-filesystem==0.31.0
termcolor==2.5.0
tifffile==2024.9.20
toolz==1.0.0
torch==2.5.1
tornado==6.1
tqdm==4.67.1
typing_extensions==4.12.2
urllib3==1.26.20
vpt @ file:///C:/Users/marsdenl/~/.venv/vizgen-postprocessing
Werkzeug==3.1.3
wrapt==1.17.0
yarl==1.18.0
zict==3.0.0

[marsdenl]

Turns out the issue was linked to the file system separator. Managed to move past it now but realised this fork is not compatible with Cellpose 2. Are there any plans to update it for CP2 compatibility? Thank you for your help.

Luc