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RELEASE_OVERVIEW.md

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Release Overview

New in version 1.4.0

This release includes three main changes:

  • Preliminary support for automatic tracking via Trackastra integration.
  • Changes in the GUI to make the model names more informative.
  • Much easier installation on Windows.

New in version 1.3.1

Fixing minor issues with 1.3.0 and adding new section in documentation for our data submission initiative.

New in version 1.3.0

This release introduces a new light microscopy model that was trained on a larger dataset and clearly improves automatic segmentation.

New in version 1.2.2

Fixing minor issues with 1.2.1 for making automatic segmentation CLI more flexible.

New in version 1.2.1 This version introduces several changes that are part of three of our recent publications that are built on top of micro_sam:

  • medico-sam, which improves SAM for medical images
  • peft-sam, which investigates parameter efficient finetuning for SAM
  • patho-sam, which improves SAM for histopathology

New in version 1.2.0

The main changes in this version are:

  • Installation using only conda-forge dependencies and simplified installation instructions (on Linux and Mac OS).
  • Fix annotation in napari widgets with scale factors.
  • Support for several parameter-efficient training methods.

New in version 1.1.1

Fixing minor issues with 1.1.0 and enabling pytorch 2.5 support.

New in version 1.1.0

This version introduces several improvements:

  • Bugfixes and several minor improvements
  • Compatibility with napari >=0.5
  • Automatic instance segmentation CLI
  • Initial support for parameter efficient fine-tuning and automatic semantic segmentation in 2d and 3d (not available in napari plugin, part of the python library)

New in version 1.0.1

Use stable URL for model downloads and fix issues in state precomputation for automatic segmentation.

New in version 1.0.0

This release mainly fixes issues with the previous release and marks the napari user interface as stable.

New in version 0.5.0

This version includes a lot of new functionality and improvements. The most important changes are:

  • Re-implementation of the annotation tools. The tools are now implemented as napari plugin.
  • Using our improved functionality for automatic instance segmentation in the annotation tools, including automatic segmentation for 3D data.
  • New widgets to use the finetuning and image series annotation functionality from napari.
  • Improved finetuned models for light microscopy and electron microscopy data that are available via bioimage.io.

New in version 0.4.1

  • Bugfix for the image series annotator. Before the automatic segmentation did not work correctly.

New in version 0.4.0

  • Significantly improved model finetuning
  • Update the finetuned models for microscopy, see details in the doc
  • Training decoder for direct instance segmentation (not available via the GUI yet)
  • Refactored model download functionality using pooch

New in version 0.3.0

  • Support for ellipse and polygon prompts
  • Support for automatic segmentation in 3d
  • Training refactoring and speed-up of fine-tuning

New in version 0.2.1 and 0.2.2

  • Several bugfixes for the newly introduced functionality in 0.2.0.

New in version 0.2.0

  • Functionality for training / finetuning and evaluation of Segment Anything Models
  • Full support for our finetuned segment anything models
  • Improvements of the automated instance segmentation functionality in the 2d annotator
  • And several other small improvements

New in version 0.1.1

  • Fine-tuned segment anything models for microscopy (experimental)
  • Simplified instance segmentation menu
  • Menu for clearing annotations

New in version 0.1.0

  • We support tiling in all annotators to enable processing large images.
  • Implement new automatic instance segmentation functionality:
    • That is faster.
    • Enables interactive update of parameters.
    • And also works for large images by making use of tiled embeddings.
  • Implement the image_series_annotator for processing many images in a row.
  • Use the data hash in pre-computed embeddings to warn if the input data changes.
  • Create a simple GUI to select which annotator to start.
  • And made many other small improvements and fixed bugs.

New in version 0.0.2

  • We have added support for bounding box prompts, which provide better segmentation results than points in many cases.
  • Interactive tracking now uses a better heuristic to propagate masks across time, leading to better automatic tracking results.
  • And have fixed several small bugs.