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.gitignore
CARE
- CARE.py
CycleGAN
- CycleGAN.py
- CycleGAN_LossFunctions.py
- CycleGAN_Model.py
- CycleGAN_Optimizers.py
- __init__.py
- cycleGun_scratch.ipynb
- cycleGun_scratch.py
LICENSE
Noise2Void
- noise2gun.py
- noise2gun_interactive.ipynb
README.md
Segmentation
- batch_apply_affinities.sh
- batch_train_affinities.py
- default
- mknet.py
- rasterize_skeleton.py
- reject.py
- train_affinity.py
SliceFill
- SliceFill.py
- SliceFill_LossFunctions.py
- SliceFill_Models.py
- SliceFill_Optimizers.py
- __init__.py
Utils
- __init__.py
- alignment.py
- cgan_eval_tools.py
- downsample_GC.py
- make_foreground_mask.py
- make_min_affs_layer.py
- make_zarr_cutout.py
- metrics
  - test_thresh_metrics.json
- ng_view_zarr.py
- render_CycleGAN.py
- segment_eval_tools.py
- smooth_segmentation.py
- upload_zarr.py
- wkw_seg_to_zarr.py
__init__.py
boilerPlate.py
cgan_compare.py
compare.py
compare_interactive.py
dnet_testing.py
example_scripts
- add_validation_mask.py
- cloudvolume_to_zarr.py
- example_compare_script.py
- example_gunnoise_script.py
- example_make_cutout_script.py
- example_rendering_script.py
- example_training_script.py
- example_validation_mask.sh
- raw_to_zarr.py
- rechunk_script.sh
- run_tb.sh
- tif_to_zarr.sh
gunnoise.py
gunnoise_interactive.py
ij-raw2n5-howto.txt
jeff_utils.py
loser.py
manu_scripts
- CBv30nmBottom100um_make_mask.py
- CBv30nmBottomAffMin_trainingCutout.py
- CBv30nmBottom_trainingCutout.py
- CBv90nmBottom_trainingCutout.py
- CBv90nmOverview_make_mask.py
- CBvRenderNetOutputs.py
- CBvRenderNetOutputs.sbatch
- CBvRenderNetOutputs_LinkSeed13_Minimal.sbatch
- CBvRenderNetOutputs_LinkSeed42_Minimal.sbatch
- CBvRenderNetOutputs_LinkSeed4_Minimal.sbatch
- CBvRenderNetOutputs_Minimal.py
- CBvRenderNetOutputs_SplitSeed13_Minimal.sbatch
- CBvRenderNetOutputs_SplitSeed3_Minimal.sbatch
- CBvRenderNetOutputs_SplitSeed42.sbatch
- CBvRenderNetOutputs_SplitSeed42_Minimal.sbatch
- CBvRenderNetOutputs_SplitSeed42_Minimal350000.sbatch
- CBvRenderNetOutputs_SplitSeed42_tiled.sbatch
- CBvRenderNetOutputs_all_tiled.sbatch
- CBx30nm_8um_1_cutout_script.py
- CBxFN90nmTile2_make_mask.py
- EM2XNH_noiseDict.json
- TransformParameters.0.txt
- TransformParameters.1.txt
- bilinear_upsample_90to30nm.py
- cb2_gcl1_cutout_script.py
- cb2_myelGCL1_affs_cutout_script.py
- cb2_myelGCL1_cutout_script.py
- cb2_myelWM1_affs_cutout_script.py
- cb2_myelWM1_cutout_script.py
- convert_CBxFN.ijm
- convert_CBxFN.sh
- fuse_CBxFN.ijm
- fuse_CBxFN.sh
- fuse_CBxFN_entropy.ijm
- fuse_CBxFN_entropy.sbatch
- noise_cb2.py
- qualitative_figs.py
- render.py
- render_all.py
- render_debugging.py
- rerender_all.py
- smooth_segmentation_dev.py
- train_noiser.py
phase_retrieval
- Siemens_star.svg.png
- data.py
- example_ESRF_data
  - CBxs_lobV_bottomp100um_30nm_1_
  - CBxs_lobV_bottomp100um_30nm_2_
  - CBxs_lobV_bottomp100um_30nm_3_
  - CBxs_lobV_bottomp100um_30nm_4_
  - CBxs_lobV_bottomp100um_30nm_
    - CBxs_lobV_bottomp100um_30nm_rectwopassdb9_0000.edf
- losses.py
- models.py
- phase_retrieval_dev.ipynb
- phase_retrieval_dev.py
- phase_retrieval_real.py
- plots.py
- steps.py
- utils.py
requirements.txt
scratch
- freezeNorm.py
segway
- __pycache__
  - __init__.cpython-36.pyc
  - __init__.cpython-37.pyc
- add_to_path.sh
- batch_checkpoints.py
- evaluation
- fix
- gt_scripts
- myelin_scripts
- synapse_evaluation
- synful_tasks
- tasks
- tools
setup.py
src/raygun
- __init__.py
- io
- torch
  - __init__.py
  - default_configs
    - blank_conf.json
    - default_cycleGAN_conf.json
  - losses
  - models
  - networks
  - optimizers
  - predict
  - systems
  - train
  - utils
- utils.py
tests
- __init__.py
- torch
  - __init__.py
  - systems
    - CycleGAN_test.py
utils.py

473 files changed

+4828

-54253

lines changed

`‎.gitignore‎`

-Original file line number
+Diff line change
@@ @@ -1,13 +1,4 @@ @@
 -events.out.tfevents.*
 -*checkpoint*
 -.vscode*
 *__pycache__*
 -*.zarr
 -*Task*.config
 -.run_configs*
 -.daisy_logs_BlockwiseTask*
 -*.out
 -.nfs*
 -*/igneous_tasks
 -TransformParameters*
 -raygun.egg*
 +*raygun.egg*
 +experiments/*
 +old_src/*

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