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Updates to public quilt data #166

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Updates to public quilt data #166

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4356645
Added sum projection-related feature
vianamp Oct 23, 2020
5fe6f5f
Loop over all FOVS
vianamp Oct 23, 2020
23f82c6
Adjusts to run the live fixed comparison
vianamp Nov 9, 2020
166eb2f
Patch for downloading dataset from public Quilt
vianamp Feb 11, 2022
3882bca
Updated model quilt address for inference
vianamp Feb 16, 2022
2382501
remove test dataset downloading
mfs4rd Sep 23, 2024
6732c1c
updates to data paths
mfs4rd Nov 4, 2024
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15 changes: 11 additions & 4 deletions .gitignore
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Expand Up @@ -115,7 +115,14 @@ venv.bak/
.mypy_cache/

# Results from assay-dev
./fish_morphology_code/processing/structure_organization/local_organization/train/data/
./fish_morphology_code/processing/structure_organization/local_organization/train/patches/
./fish_morphology_code/processing/structure_organization/output/
./fish_morphology_code/processing/structure_organization/results/
*.csv
fish_morphology_code/processing/structure_organization/local_organization/best_model
fish_morphology_code/processing/structure_organization/local_organization/train/data
fish_morphology_code/processing/structure_organization/local_organization/train/models
fish_morphology_code/processing/structure_organization/local_organization/train/patches
fish_morphology_code/processing/structure_organization/global_alignment/jinja2
fish_morphology_code/processing/structure_organization/tools/jinja2
fish_morphology_code/processing/structure_organization/notebooks/figs
fish_morphology_code/processing/structure_organization/output*
fish_morphology_code/processing/structure_organization/results*

5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -39,7 +39,7 @@ contrast_and_segment quilt_data/metadata.csv quilt_data/supporting_files/channel

### Running cellprofiler to calculate single cell shape and texture features

Before running cellprofiler, download auto-contrasted images from quilt (ex. ```download_2D_contrasted --test=True```) into current working directory.
Before running cellprofiler, download auto-contrasted images from quilt (ex. ```download_2D_contrasted```) into current working directory.

Create an image set list in format accepted by cellprofiler's LoadData module.
```
Expand All @@ -48,7 +48,8 @@ make_cellprofiler_image_set \
--defaults_json fish_morphology_code/cellprofiler/cellprofiler_image_set_defaults.json \
--path_key rescaled_2D_fov_tiff_path \
--local_path ./quilt_data_contrasted_test \
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Should we remove test from the path since there is no longer a test set?

--out_loc ./test_image_set_list.csv
--out_loc ./test_image_set_list.csv \
--fish_type structure
```

Run cellprofiler pipeline in this repository using test image set list as input:
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