0.4.1

The main feature of release v0.4.1 is the addition of imagecodecs to support processing of compressed OME tiff files.

🧰 Maintenance

Bump dependencies to support compressed OME TIFs @rossbar (#36)

Add imagecodecs to requirements.

Also includes a temporary pin for scikit-image to avoid issues with the latest release.

General maintenance of test infrastructure @rossbar (#34)

Similar to vanvalenlab/deepcell-tf#639, minus the explicit add for Python 3.10 support which will need to wait for another deepcell-tf release.

Update default actions to latest version. @rossbar (#33)

Rm deprecation warnings in action logs. See also: vanvalenlab/deepcell-tf#653

0.4.0

This release includes the updated Mesmer model that was released in the most recent deepcell-tf build. It provides better nuclear segmentation in areas without true cells. It also has a slight tweak to the post-processing for cell segmentation to better balance between segmentation errors and inclusion of cell area.

Pre-release updates @ngreenwald (#29)

Update to new Mesmer model @ngreenwald (#28)

0.3.1

🐛 Bug Fixes

Add "both" to the argument parser. @willgraf (#25)

Adds "both" as a valid value for --compartment to better match the model and removes "membrane".

Fixes #24

🧰 Maintenance

Adding testing for argparse @ngreenwald (#22)

We currently don't test the argparse functionality in the repo. This PR moves the argparse function to utils and adds testing to make sure parameters are passed appropriately, and that errors are raised when required.

0.3.0

🐛 Bug Fixes

Update docker image to use deepcell 0.10.0 @willgraf (#21)

#18 updated the deepcell version in requirements.txt but did NOT update the version in the GHA release configuration. This means that the 0.2.x builds are using deepcell 0.9.1 instead of the latest release 0.10.0.

0.2.1

🐛 Bug Fixes

Add `--squeeze` to all the child subparsers. @willgraf (#20)

--squeeze was added as an optional argument in #17, but it was added to the main argument parser instead of the parent. This means that the mesmer command does not recognize it.

This PR resolves the issue by adding it to the parent argparser instead of the primary one. This allows mesmer and all other subparsers to inherit the --squeeze arg.

0.2.0

🚀 Features

Add `--squeeze` to CLI arguments. @willgraf (#17)

If passed, call np.squeeze on the output tensor before saving as a tiff.

Closes #16

🐛 Bug Fixes

pip install coveralls in GHA workflows. @willgraf (#19)

🧰 Maintenance

pip install coveralls in GHA workflows. @willgraf (#19)

Upgrade DeepCell to version 0.10.0 @willgraf (#18)

The latest release of DeepCell (0.10.0) fixes several performance issues including:

• improved batching in the Applications
• Support individual parameter passing to Mesmer application
• Allow preprocessing_fn and postprocessing_fn to be overridden.
• Update Tensorflow to 2.5.1 (fixes several vulnerabilities).

0.1.0

0.1.0

Features

• New deepcell_applications module with fully tested application helper functions
• Support multiple channels from a single channel via nuclear-channel and membrane-channel
• Enable multiple applications via argparse subparsers and Application class name
• Add GitHub Actions workflows for testing, docker image builds, and release drafts

Bugfixes

• Pin deepcell~=0.9.2 and fix get_image imports