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Merged
mese79 merged 35 commits into from
Jun 22, 2025
Merged

Major updates! #44

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2891520
added No Patching checkbox to extractor widget
mese79 Jun 11, 2025
ca67604
updated models adapters to support no_patching
mese79 Jun 11, 2025
cb3d544
updated segmentation widget
mese79 Jun 12, 2025
411bd9e
removed unused imports
mese79 Jun 12, 2025
b9ce247
fixed some typings
mese79 Jun 12, 2025
2050125
added the dataset class
mese79 Jun 12, 2025
928cdb0
init using the new dataset for feature extraction
mese79 Jun 12, 2025
1ce1ea0
init using zarr storage
mese79 Jun 13, 2025
123bfd9
moved up no patching checkbox
mese79 Jun 13, 2025
2d8d91e
updated extractor widget and no_patching option
mese79 Jun 13, 2025
b5e6edf
updated segmentation widget using zarr storage
mese79 Jun 13, 2025
3b68f8c
clean up & formatting
mese79 Jun 13, 2025
2999421
fixed extraction progress info
mese79 Jun 13, 2025
75f80e4
updated dataset to handle images type inside
mese79 Jun 13, 2025
7f5b78c
updated prediction pipeline over a large stack
mese79 Jun 14, 2025
5bfe8c9
fixed run pipeline; file dialogs open in parent dialog
mese79 Jun 14, 2025
6393b2a
updated run_pipeline script
mese79 Jun 15, 2025
e959bf1
removed unused import in run_pipeline
mese79 Jun 15, 2025
b580968
fixed models params: image height & width as int
mese79 Jun 15, 2025
b7261df
ignored some typing
mese79 Jun 15, 2025
bc624a2
updated requirements
mese79 Jun 15, 2025
b3d6720
fixed image height & width as int
mese79 Jun 15, 2025
32f4a26
fixed dataset & get_model_ready_image image dimention problem
mese79 Jun 15, 2025
f2b04d6
added dataset test
mese79 Jun 15, 2025
0104b10
fixed adapter: concat double output into one tensor
mese79 Jun 15, 2025
8b9cc93
updated mobilesam test
mese79 Jun 15, 2025
f4c6239
updated dino adapter test
mese79 Jun 15, 2025
227a8d4
added sam2 adapter test
mese79 Jun 15, 2025
b3bd256
added pipeline_prediction test
mese79 Jun 15, 2025
d3fce05
bumped version
mese79 Jun 15, 2025
5eb9ed0
run_pipeline script can be used to only extract features
mese79 Jun 15, 2025
0cc7b37
updated dependencies in pyproject.toml
mese79 Jun 18, 2025
1118177
fixed bug for calculating padding with no_patching
mese79 Jun 18, 2025
10acde5
revert back storage to hdf5; improved get_train_data
mese79 Jun 20, 2025
d26ae91
fixed embedding_extraction test
mese79 Jun 20, 2025
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4 changes: 3 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,9 @@ dependencies = [
"qtpy",
"magicgui",
"napari[all]",
"h5py",
"tifffile",
"zarr>=2,<3",
"pims",
"pooch",
"tqdm>=4.66.1",
"iopath>=0.1.10",
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4 changes: 3 additions & 1 deletion requirements.txt
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Expand Up @@ -9,7 +9,9 @@ pynrrd
qtpy
magicgui
napari[all]
h5py
tifffile
zarr>=2,<3
pims
pooch
tqdm>=4.66.1
iopath>=0.1.10
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