Releases: mehta-lab/VisCy
v0.2.1
Patch release to update README and example notebooks.
What's Changed
- version lighting CLI example by @mattersoflight in #128
- Updated code (contrastive learning) by @alishbaimran in #130
- Configurable drop path rate in contrastive models by @ziw-liu in #131
- Config-based prediction with Xarray-based output format by @ziw-liu in #132
- Plot tracks in latent space and real space by @mattersoflight in #135
- Fix deprecated custom forward method by @ziw-liu in #151
- updating the notebook after running it at DLMBL2024 by @edyoshikun in #149
Full Changelog: v0.2.0...v0.2.1
VisCy 0.2.0
VisCy 0.2.0 adds the following features:
- Application scripts for single-cell infection classification through semantic segmentation
- Tutorial notebook that demonstrates the virtual staining pipeline
- Test time augmentations in the virtual staining prediction writer
- (Alpha) Experimental support for single-cell phenotyping through contrastive learning
This release maintains compatibility with the virtual staining model weights from the v0.1.0 release (download link).
What's Changed
- Update dataset URL for demos by @ziw-liu in #103
- Bump lightning and matplotlib by @ziw-liu in #105
- Cellular infection phenotyping using annotated viral sensor data & label-free images by @Soorya19Pradeep in #70
- Pin numpy due to MONAI bug by @ziw-liu in #111
- Updating demo notebook for training by @edyoshikun in #100
- Test time augmentations by @edyoshikun in #91
- Update demo setup script by @ziw-liu in #112
- Single-cell phenotyping with contrastive learning by @ziw-liu in #113
- Migrate from wandb to tensorboard by @ziw-liu in #122
- Adding link to demos and library of VS models wiki by @edyoshikun in #119
- Tune augmentations with CLI and config for contrastive models by @ziw-liu in #126
- DLMBL 2024 notebook by @edyoshikun in #114
New Contributors
- @Soorya19Pradeep made their first contribution in #70
Full Changelog: v0.1.1...v0.2.0
VisCy 0.2.0rc0
VisCy 0.2.0 adds the following features:
- Application scripts for single-cell infection classification through semantic segmentation
- Tutorial notebook that demonstrates the virtual staining pipeline
- Test time augmentations in the virtual staining prediction writer
This release maintains compatibility with the virtual staining model weights from the v0.1.0 release (download link).
What's Changed
- Update dataset URL for demos by @ziw-liu in #103
- Bump lightning and matplotlib by @ziw-liu in #105
- Cellular infection phenotyping using annotated viral sensor data & label-free images by @Soorya19Pradeep in #70
- Pin numpy due to MONAI bug by @ziw-liu in #111
- Updating demo notebook for training by @edyoshikun in #100
- Test time augmentations by @edyoshikun in #91
New Contributors
- @Soorya19Pradeep made their first contribution in #70
Full Changelog: v0.1.1...v0.2.0rc0
VisCy 0.1.1
VisCy 0.1.0
This is first release of VisCy, the machine learning pipeline to train and deploy computer vision models for single-cell phenotyping.
With 0.1.0 the following key features are available:
- Training, evaluation, inference, and deployment of virtual staining models based on 2D Residual U-Net, 2.5D U-Net, 3D U-Net, and UNeXt2 architectures
- Data module implementations for HCS OME-Zarr datasets, as well public test datasets like LiveCell and CTMC v1.
- Composing datasets and transformations for training and validation
- Distributed (DDP) training
The weights of the virtual staining models reported in the preprint can be found in the binaries section below.
What's Changed
- Migration from microDL by @ziw-liu in #1
- Update README by @ziw-liu in #22
- Bump iohub version by @ziw-liu in #25
- readme + dependencies tested with python 3.10 by @mattersoflight in #30
- Demo notebooks by @ziw-liu in #29
- 3D augmentation and 2.1D U-Net by @ziw-liu in #27
- Fix datamodule by @ziw-liu in #28
- Improve augmentation by @ziw-liu in #31
- Fix inference by @ziw-liu in #32
- viscy -> VisCy by @mattersoflight in #34
- Update readme.md typo for
cd VisCy
by @edyoshikun in #41 - 2.1D upscale decoder by @ziw-liu in #37
- dlmbl 2023 archive by @mattersoflight in #44
- Fix center slice metrics for 3D output by @ziw-liu in #51
- Configure the number of image samples logged at each epoch and batch by @ziw-liu in #49
- Example workflow by @ziw-liu in #45
- Project icon by @ziw-liu in #38
- Fix predicting new channels in an existing store by @ziw-liu in #57
- Document data methods by @ziw-liu in #50
- Visualize feature maps by @ziw-liu in #53
- Baseline 3D-LUNeXt by @ziw-liu in #58
- Preprocess CLI and source scaling during prediction by @ziw-liu in #59
- Configurable augmentations by @ziw-liu in #61
- Bump dependencies and update documentation by @ziw-liu in #64
- checkpoint as a model config parameter for warmup cosine learning rates by @edyoshikun in #66
- Masked autoencoder pre-training for virtual staining models by @ziw-liu in #67
- Filter empty detections in labels by @ziw-liu in #74
- Add CITATION.cff by @ziw-liu in #79
- Fix 3D to 2D prediction with UNeXt2 model by @ziw-liu in #80
- 2D FCMAE by @ziw-liu in #71
- Rename UNeXt2 by @ziw-liu in #84
- Test on Python 3.12 by @ziw-liu in #88
- Add preprint reference to README by @ziw-liu in #85
- Fix architecture name in network diagram script by @ziw-liu in #86
- Add the scale metadata to the output_stores by @edyoshikun in #89
- bumping to cellpose 3 by @edyoshikun in #92
- Scale metadata handling for positions by @edyoshikun in #93
- Demo for VSCyto2D and VSCyto3D by @edyoshikun in #94
- Fix demos on other platforms by @ziw-liu in #95
Full Changelog: https://github.com/mehta-lab/VisCy/commits/v0.1.0