Releases | Open Source Science

spotiflow - 0.5.8

What's Changed

Added support for OME-Zarr prediction in CLI
Add --channels argument to training and prediction CLI for channel selection by @qin-yu in https://github.com/weigertlab/spotiflow/pull/39
Example notebook fix
Fix 3D Gaussian fit
Bump Windows version for CI

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.7...0.5.8

- Python
Published by AlbertDominguez 5 months ago

spotiflow - Bugfix: 3D multi-channel training

Fix multi-channel 3D volume handling by @qin-yu in https://github.com/weigertlab/spotiflow/pull/34

New Contributors

@qin-yu made their first contribution in https://github.com/weigertlab/spotiflow/pull/34

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.6...0.5.7

- Python
Published by AlbertDominguez 7 months ago

spotiflow - Bugfix: multi-channel training

Fixed bug causing multi-channel training not to work
Fixed bug where training crashed if an explicit SpotiflowTrainingConfig instance was passed as the train_params argument to the Spotiflow.fit() method.
Fixed tests.

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.5...0.5.6

- Python
Published by AlbertDominguez 7 months ago

spotiflow - 0.5.5

What's Changed

Remove verbosity argument in scheduler by @anwai98 in https://github.com/weigertlab/spotiflow/pull/30
better augmentation api;data loading by @maweigert in https://github.com/weigertlab/spotiflow/pull/29
fixed model 3d training argument
CLI defaults to point priority sampling for training

New Contributors

@anwai98 made their first contribution in https://github.com/weigertlab/spotiflow/pull/30

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.4...0.5.5

- Python
Published by AlbertDominguez 7 months ago

spotiflow - 0.5.4

Add support for numpy>=2.0 (#28)
Add support for Python 3.13

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.3...0.5.4

- Python
Published by AlbertDominguez 10 months ago

spotiflow - 0.5.3

Fixed #26, #27
Default default to more likely sampling of patches containing spots (at least 80% of them)
Added 2D+t sample data

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.2...0.5.3

- Python
Published by AlbertDominguez 10 months ago

spotiflow - 0.5.2

Updated starfish integration module
Avoid extracting zipped pre-trained model if already extracted (#23)

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.1...0.5.2

- Python
Published by AlbertDominguez 12 months ago

spotiflow - 0.5.1

What's Changed

Fix 3D tiled flow inference
Fix explicit augmentation parameter passing to the fit method.
Add spots fitting option to CLI to retrieve spot size
Improve probability threshold optimization
Tweak training scripts
Move flow normalization to the forward pass

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.5.0...0.5.1

- Python
Published by AlbertDominguez about 1 year ago

spotiflow - 0.5.0

What's Changed

Extend NMS behaviour
Changes to CLI arguments for readability
Added option to train from the CLI
Documentation improvement

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.4.5...0.5.0

- Python
Published by AlbertDominguez about 1 year ago

spotiflow - 0.4.5

Downgrade CI actions (#18)

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.4.4...0.4.5

- Python
Published by AlbertDominguez about 1 year ago

spotiflow - 0.4.4

Added support for Python 3.12 by dropping distutils from wheel building.
Bump docs version automatically when building the docs
Fix API display in docs

Full Changelog: https://github.com/weigertlab/spotiflow/compare/0.4.3...0.4.4

- Python
Published by AlbertDominguez about 1 year ago