viscy-transforms
Image transforms for virtual staining microscopy.
Part of the VisCy project.
Installation
From PyPI (when published)
pip install viscy-transforms
For development (from monorepo root)
# Using uv (recommended)
uv pip install -e packages/viscy-transforms
# Or via workspace sync
uv sync --package viscy-transforms
Usage
from viscy_transforms import NormalizeSampled, BatchedRandAffined
# Transforms follow MONAI dictionary transform pattern
# See documentation for full API reference
Features
- PyTorch-based image transforms optimized for microscopy data
- MONAI Dictionary transform compatibility for DataLoader pipelines
- Kornia-accelerated augmentations (affine, noise, blur)
- Specialized transforms for virtual staining workflows
Examples
To run the example notebook, install with the notebook extra:
pip install viscy-transforms[notebook]
See the batched transforms benchmark notebook for a comparison of batched GPU transforms vs standard MONAI transforms.
Dependencies
torch>=2.4.1korniamonai>=1.4numpy
Documentation
In the works!
License
BSD-3-Clause - see LICENSE in repository root.
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file viscy_transforms-0.1.0.tar.gz.
File metadata
- Download URL: viscy_transforms-0.1.0.tar.gz
- Upload date:
- Size: 6.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
eba7ea12edc155d3724009656d4670ce928429c5d87acce30a8b57987dbd5dc3
|
|
| MD5 |
cf209007d3fb1fadebedb82261fc9512
|
|
| BLAKE2b-256 |
86d32904b87395e4171cb994dacf5f020260aaef5760741c741a729e9b69dddf
|
Provenance
The following attestation bundles were made for viscy_transforms-0.1.0.tar.gz:
Publisher:
release.yml on mehta-lab/VisCy
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
viscy_transforms-0.1.0.tar.gz -
Subject digest:
eba7ea12edc155d3724009656d4670ce928429c5d87acce30a8b57987dbd5dc3 - Sigstore transparency entry: 2537837649
- Sigstore integration time:
-
Permalink:
mehta-lab/VisCy@4b62365c0df25929bffc7f01b3bb2d1c11d69cce -
Branch / Tag:
refs/tags/viscy-transforms-v0.1.0 - Owner: https://github.com/mehta-lab
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
release.yml@4b62365c0df25929bffc7f01b3bb2d1c11d69cce -
Trigger Event:
release
-
Statement type:
File details
Details for the file viscy_transforms-0.1.0-py3-none-any.whl.
File metadata
- Download URL: viscy_transforms-0.1.0-py3-none-any.whl
- Upload date:
- Size: 45.8 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
1716fb9dfb99cb51c8c26c698902138810b0f7d62bfc878149026e6888192870
|
|
| MD5 |
a76100f094743826513c3358c6c6ee64
|
|
| BLAKE2b-256 |
5eb2f29a4cd2879dd4428a4c1b3e2f9f8529bbbd9eeb5093ee8b6c7f1d050974
|
Provenance
The following attestation bundles were made for viscy_transforms-0.1.0-py3-none-any.whl:
Publisher:
release.yml on mehta-lab/VisCy
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
viscy_transforms-0.1.0-py3-none-any.whl -
Subject digest:
1716fb9dfb99cb51c8c26c698902138810b0f7d62bfc878149026e6888192870 - Sigstore transparency entry: 2537838928
- Sigstore integration time:
-
Permalink:
mehta-lab/VisCy@4b62365c0df25929bffc7f01b3bb2d1c11d69cce -
Branch / Tag:
refs/tags/viscy-transforms-v0.1.0 - Owner: https://github.com/mehta-lab
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
release.yml@4b62365c0df25929bffc7f01b3bb2d1c11d69cce -
Trigger Event:
release
-
Statement type:
