.gitignore
.gitmodules
.readthedocs.yaml
LICENSE
MANIFEST.in
README.md
logo.png
logo2.png
logo3.png
setup.py
test_omni.py
tox.ini
docs/.DS_Store
docs/command.ipynb
docs/conf.py
docs/diameter.rst
docs/gamma.ipynb
docs/gui.rst
docs/index.rst
docs/inputs.rst
docs/installation.rst
docs/links.rst
docs/logo.ipynb
docs/ncolor.ipynb
docs/notebook.rst
docs/outputs.rst
docs/requirements.txt
docs/settings.rst
docs/sinebow.rst
docs/_static/cellpose_gui.png
docs/_static/cellpose_to_imagej.gif
docs/_static/custom.css
docs/_static/ex_seg.png
docs/_static/favicon.ico
docs/_static/fig1.PNG
docs/_static/icon.png
docs/_static/logo.png
docs/_templates/layout.html
docs/_templates/page.html
docs/api/cellpose.rst
docs/api/index.rst
docs/api/omnipose.rst
docs/examples/.DS_Store
docs/examples/img02.png
docs/examples/mono_channel_bact.ipynb
docs/examples/multi_channel_cyto.ipynb
docs/test_files/.DS_Store
docs/test_files/Sample000033.png
docs/test_files/Sample000193.png
docs/test_files/Sample000252.png
docs/test_files/Sample000306.tiff
docs/test_files/caulo_15.tif
docs/test_files/e1t1_crop.tif
docs/test_files/ec_5I_t141xy5c1.tif
docs/test_files/masks/Sample000033_cp_masks.tif
docs/test_files/masks/Sample000193_cp_masks.tif
docs/test_files/masks/Sample000252_cp_masks.tif
docs/test_files/masks/Sample000306_cp_masks.tif
docs/test_files/masks/caulo_15_cp_masks.tif
docs/test_files/masks/e1t1_crop_cp_masks.tif
docs/test_files/masks/ec_5I_t141xy5c1_cp_masks.tif
gui/gamma.svg
gui/icon.png
gui/logo.png
omnipose/__init__.py
omnipose/__main__.py
omnipose/core.py
omnipose/utils.py
omnipose/__pycache__/__init__.cpython-38.pyc
omnipose/__pycache__/core.cpython-38.pyc
omnipose/__pycache__/core.cpython-39.pyc
omnipose/__pycache__/utils.cpython-38.pyc
omnipose/__pycache__/utils.cpython-39.pyc
omnipose_acdc.egg-info/PKG-INFO
omnipose_acdc.egg-info/SOURCES.txt
omnipose_acdc.egg-info/dependency_links.txt
omnipose_acdc.egg-info/requires.txt
omnipose_acdc.egg-info/top_level.txt
plugins/README.md
plugins/cellprofiler_plugins_mac.yml
plugins/runomnipose.py
plugins/setup.py
pyinstaller/omni.py
scripts/.DS_Store
scripts/3D_omnipose.ipynb
scripts/Diameter_metric.ipynb
scripts/Figure_1.ipynb
scripts/Figure_2A_4AB_CP_OM_Compare.ipynb
scripts/Figure_3_S5.ipynb
scripts/Figure_5_S6_Tre1.ipynb
scripts/Figure_6_C_elegans_cyto2.ipynb
scripts/Figure_6_cyto2_example.ipynb
scripts/Figure_6_fluroescence.ipynb
scripts/Figure_6_worm_high_res.ipynb
scripts/Figure_S2.ipynb
scripts/Figure_S3.ipynb
scripts/Figure_S5.ipynb
scripts/Figure_S7.ipynb
scripts/Figure_SX_DeLTA.ipynb
scripts/Figures_3_4_S1.ipynb
scripts/Ground_truth_export_and_thumbnails.ipynb
scripts/LICENSE
scripts/README.md
scripts/export_models.ipynb
scripts/ftsN_comparison.eps
scripts/ftsN_comparison.png
scripts/image_cell_counting.ipynb
scripts/img02.png
scripts/scale_bars.ipynb
scripts/BBBC027/Untitled.ipynb
scripts/BBBC027/bbbc.ipynb
scripts/Cellpose/.DS_Store
scripts/Cellpose/Figure_6_C_elegans-Copy1-convert to all.ipynb
scripts/Cellpose/README.md
scripts/Cellpose/comparisons.ipynb
scripts/Cellpose/comparisons_OGdata.ipynb
scripts/Cellpose/comparisons_c_elegans.ipynb
scripts/Cellpose/comparisons_final_bacteria.ipynb
scripts/Cellpose/train_size.ipynb
scripts/DeLTA/.DS_Store
scripts/DeLTA/DeLTA.ipynb
scripts/DeLTA/README.md
scripts/Mask R-CNN/.DS_Store
scripts/Mask R-CNN/Mask R-CNN torchvision-Copy1.ipynb
scripts/Mask R-CNN/Mask R-CNN torchvision.ipynb
scripts/Mask R-CNN/README.md
scripts/Mask R-CNN/coco_eval.py
scripts/Mask R-CNN/coco_utils.py
scripts/Mask R-CNN/engine.py
scripts/Mask R-CNN/group_by_aspect_ratio.py
scripts/Mask R-CNN/train.py
scripts/Mask R-CNN/transforms.py
scripts/Mask R-CNN/utils.py
scripts/MiSiC/.DS_Store
scripts/MiSiC/Figure_1_misic.ipynb
scripts/MiSiC/misic_Tre1_Figure6.ipynb
scripts/MiSiC/misic_retraining_script.ipynb
scripts/MiSiC/new_misic_model_kevin_ep100_bs8.h5
scripts/Morphometrics/README.md
scripts/Morphometrics/mm_settings.png
scripts/PlantSeg/Export_slices.ipynb
scripts/PlantSeg/Figure_6_plantseg_root.ipynb
scripts/PlantSeg/plantseg_root.ipynb
scripts/StarDist/.DS_Store
scripts/StarDist/2_training_kevin.ipynb
scripts/StarDist/3_prediction_kevin.ipynb
scripts/StarDist/3_prediction_kevin_Tre1_Figure_6.ipynb
scripts/StarDist/README.md
scripts/StarDist/models/.DS_Store
scripts/StarDist/models/stardist/.DS_Store
scripts/StarDist/models/stardist/config.json
scripts/StarDist/models/stardist/thresholds.json
scripts/StarDist/models/stardist/weights_best.h5
scripts/StarDist/models/stardist/weights_last.h5
scripts/StarDist/models/stardist/logs/.DS_Store
scripts/StarDist/models/stardist/logs/images/events.out.tfevents.1628048234.kevin-desktop.5271.1394.v2
scripts/StarDist/models/stardist/logs/images/events.out.tfevents.1628048905.kevin-desktop.5271.16421.v2
scripts/StarDist/models/stardist/logs/train/events.out.tfevents.1628048234.kevin-desktop.5271.1439.v2
scripts/StarDist/models/stardist/logs/train/events.out.tfevents.1628048314.kevin-desktop.5271.6381.v2
scripts/StarDist/models/stardist/logs/train/events.out.tfevents.1628048905.kevin-desktop.5271.16466.v2
scripts/StarDist/models/stardist/logs/validation/events.out.tfevents.1628048238.kevin-desktop.5271.4144.v2
scripts/StarDist/models/stardist/logs/validation/events.out.tfevents.1628048317.kevin-desktop.5271.6538.v2
scripts/StarDist/models/stardist/logs/validation/events.out.tfevents.1628048933.kevin-desktop.5271.19801.v2
scripts/SuperSegger/SuperSegger_test_dataset_evaluation.mlx