Releases: mehta-lab/VisCy
VisCy 0.3.2
Note
Our paper Robust virtual staining of landmark organelles with Cytoland is now published in Nature Machine Intelligence!
This version of VisCy is compatible with the models and demos described in the paper.
This release includes maintenance patches and documentation improvements.
What's Changed
- Fix swapped colormap in the neuromast tutorial by @ziw-liu in #256
- Document AugmentedPredictionVSUNet by @ziw-liu in #261
- Update HF demo links by @ziw-liu in #264
- Replace black with ruff by @ziw-liu in #262
Full Changelog: v0.3.1...v0.3.2
Contributors
Assets 2
VisCy 0.3.2rc0
Warning
This is a release candidate for testing.
What's Changed
- Fix swapped colormap in the neuromast tutorial by @ziw-liu in #256
- Document AugmentedPredictionVSUNet by @ziw-liu in #261
- Update HF demo links by @ziw-liu in #264
- Replace black with ruff by @ziw-liu in #262
Full Changelog: v0.3.1...v0.3.2rc0
Contributors
Assets 2
VisCy 0.3.1
This release includes maintenance patches and documentation improvements.
What's Changed
- Add CLI tutorials for VCP by @ziw-liu in #239
- Update README.md to align with the title of the cytoland paper by @mattersoflight in #243
- Update VCP tutorials by @ziw-liu in #244
- Delay cellpose import by @ziw-liu in #245
- Add contact information by @melissawm in #248
- Add neuromast notebook by @ziw-liu in #249
- Skip broken test with pycocotools on python 3.13 by @ziw-liu in #252
- Fix DLMBL excercise setup script by @ziw-liu in #253
- Tweak VCP tutorials by @ziw-liu in #251
- Readme updates by @ziw-liu in #246
New Contributors
- @melissawm made their first contribution in #248
Full Changelog: v0.3.0...v0.3.1
Contributors
Assets 2
VisCy 0.3.1rc0
Warning
This is a release candidate for testing.
What's Changed
- Add CLI tutorials for VCP by @ziw-liu in #239
- Update README.md to align with the title of the cytoland paper by @mattersoflight in #243
- Update VCP tutorials by @ziw-liu in #244
- Delay cellpose import by @ziw-liu in #245
- Add contact information by @melissawm in #248
- Add neuromast notebook by @ziw-liu in #249
- Skip broken test with pycocotools on python 3.13 by @ziw-liu in #252
- Fix DLMBL excercise setup script by @ziw-liu in #253
- Tweak VCP tutorials by @ziw-liu in #251
- Readme updates by @ziw-liu in #246
New Contributors
- @melissawm made their first contribution in #248
Full Changelog: v0.3.0...v0.3.1rc0
Contributors
Assets 2
VisCy 0.3.0
VisCy 0.3.0 brings performance improvements to the image translation task, especially for very large datasets in distributed training. It also incorporates the representation learning task as a core feature.
Breaking change
The top-level CLI now supports both image translation and representation learning tasks. This required changes to configuration files. Concretely, data and model fields now require import paths to be specified. See the updated examples for reference on migrating existing virtual staining configs.
What's Changed
- Add script to visualize effective receptive field by @ziw-liu in #144
- adding VS hugginface demo by @edyoshikun in #172
- Single-cell representation learning by @ziw-liu in #153
- Vendor pad shape function by @ziw-liu in #189
- Fix module name spelling by @ziw-liu in #190
- Add new author to citation by @ziw-liu in #188
- Add links to hosted files and napari-iohub wiki by @ziw-liu in #192
- Bump MONAI to unpin NumPy by @ziw-liu in #194
- Add badges to readme by @ziw-liu in #197
- Simplify development installation by @ziw-liu in #198
- Fix validation loss aggregation in VSUNet by @ziw-liu in #202
- Expose prefetch_factor and persistent_worker for the HCS datamodule by @edyoshikun in #203
- Explicit target shape argument in the HCS data module by @ziw-liu in #212
- Rank nearest neighbors in embedding space by @ziw-liu in #211
- Gradio example by @edyoshikun in #158
- Adding NTXENT loss by @edyoshikun in #204
- Fix the wrong import name for pairwise_distance_matrix() by @edyoshikun in #215
- Fixing the TripletDataModule() after changes to HCSDataModule by @edyoshikun in #216
- Sharded distributed sampler for cached dataloading in DDP by @ziw-liu in #195
- Tweak README by @ziw-liu in #206
- Expose the option to not return negative samples in the triplet data module by @edyoshikun in #225
- Script to use ConvNeXt v1 Tiny as a feature extractor by @ziw-liu in #228
- Fix dice score by @ziw-liu in #230
- Evaluate existing segmentation by @ziw-liu in #213
- Check if the sliding window size is valid by @ziw-liu in #229
- Memory-mapped caching for image translation training by @ziw-liu in #218
- Update license metadata by @ziw-liu in #233
- Update supported python version range by @ziw-liu in #200
- Add DOI badge by @ziw-liu in #235
- Bump iohub by @ziw-liu in #236
- VCP tutorials by @ziw-liu in #227
- Remove outdated docs by @ziw-liu in #238
Full Changelog: v0.2.1...v0.3.0
Contributors
Assets 2
VisCy 0.3.0rc4
Contributors
Assets 2
VisCy 0.3.0rc3
Warning
This is a release candidate for testing.
What's Changed
- Script to use ConvNeXt v1 Tiny as a feature extractor by @ziw-liu in #228
- Fix dice score by @ziw-liu in #230
- Evaluate existing segmentation by @ziw-liu in #213
- Check if the sliding window size is valid by @ziw-liu in #229
- Memory-mapped caching for image translation training by @ziw-liu in #218
- Update license metadata by @ziw-liu in #233
Full Changelog: v0.3.0rc2...v0.3.0rc3
Contributors
Assets 2
VisCy 0.3.0rc2
Warning
This is a release candidate for testing.
What's Changed
- Explicit target shape argument in the HCS data module by @ziw-liu in #212
- Rank nearest neighbors in embedding space by @ziw-liu in #211
- Gradio example by @edyoshikun in #158
- Adding NTXENT loss by @edyoshikun in #204
- Fix the wrong import name for pairwise_distance_matrix() by @edyoshikun in #215
- Fixing the TripletDataModule() after changes to HCSDataModule by @edyoshikun in #216
- Sharded distributed sampler for cached dataloading in DDP by @ziw-liu in #195
- Tweak README by @ziw-liu in #206
- Expose the option to not return negative samples in the triplet data module by @edyoshikun in #225
Full Changelog: v0.3.0rc1...v0.3.0rc2
Contributors
Assets 2
VisCy 0.3.0rc1
Warning
This is a release candidate for testing.
VisCy 0.3.0 incorporates the representation learning task as a core feature.
Breaking change
The top-level CLI now supports both image translation and representation learning tasks. This required changes to configuration files. Concretely, data and model fields now require import paths to be specified. See the updated examples for reference on migrating existing virtual staining configs.
What's Changed
- Add script to visualize effective receptive field by @ziw-liu in #144
- adding VS hugginface demo by @edyoshikun in #172
- Single-cell representation learning by @ziw-liu in #153
- Vendor pad shape function by @ziw-liu in #189
- Fix module name spelling by @ziw-liu in #190
- Add new author to citation by @ziw-liu in #188
- Add links to hosted files and napari-iohub wiki by @ziw-liu in #192
- Bump MONAI to unpin NumPy by @ziw-liu in #194
- Add badges to readme by @ziw-liu in #197
- Simplify development installation by @ziw-liu in #198
- Fix validation loss aggregation in VSUNet by @ziw-liu in #202
- Expose prefetch_factor and persistent_worker for the HCS datamodule by @edyoshikun in #203
Full Changelog: v0.2.1...v0.3.0rc1
Contributors
Assets 2
VisCy 0.3.0rc0
Warning
This is a release candidate for testing.
VisCy 0.3.0 incorporates the representation learning task as a core feature.
Breaking change
The top-level CLI now supports both image translation and representation learning tasks. This required changes to configuration files. Concretely, data and model fields now require import paths to be specified. See the updated examples for reference on migrating existing virtual staining configs.
What's Changed
- Add script to visualize effective receptive field by @ziw-liu in #144
- adding VS hugginface demo by @edyoshikun in #172
- Single-cell representation learning by @ziw-liu in #153
- Vendor pad shape function by @ziw-liu in #189
- Fix module name spelling by @ziw-liu in #190
- Add new author to citation by @ziw-liu in #188
- Add links to hosted files and napari-iohub wiki by @ziw-liu in #192
Full Changelog: v0.2.1...v0.3.0rc0