claydugo / micro-sam

Segment Anything for Microscopy

SegmentAnything for Microscopy

Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively with a few clicks!

We implement napari applications for:

• interactive 2d segmentation (Left: interactive cell segmentation)
• interactive 3d segmentation (Middle: interactive mitochondria segmentation in EM)
• interactive tracking of 2d image data (Right: interactive cell tracking)

If you run into any problems or have questions regarding our tool please open an issue on Github or reach out via image.sc using the tag micro-sam and tagging @constantinpape.

Installation and Usage

You can install micro_sam via conda:

conda install -c conda-forge micro_sam napari pyqt

You can then start the micro_sam tools by running $ micro_sam.annotator in the command line.

For an introduction in how to use the napari based annotation tools check out the video tutorials. Please check out the documentation for more details on the installation and usage of micro_sam.

Contributing

We welcome new contributions!

If you are interested in contributing to micro-sam, please see the contributing guide and developer documentation. The first step is to discuss your idea in anew issue with the current developers.

Citation

If you are using this repository in your research please cite

• Our preprint
• and the original Segment Anything publication.
• If you use a vit-tiny models please also cite Mobile SAM.

Related Projects

There are a few other napari plugins build around Segment Anything:

• https://github.com/MIC-DKFZ/napari-sam (2d and 3d support)
• https://github.com/JoOkuma/napari-segment-anything (only 2d support)
• https://github.com/hiroalchem/napari-SAM4IS

Compared to these we support more applications (2d, 3d and tracking), and provide finetuning methods and finetuned models for microscopy data. WebKnossos also offers integration of SegmentAnything for interactive segmentation.

Release Overview

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.