Segmentation with micro-sam
Segment Anything for Microscopy or micro-sam is a tool to enable automatic and interactive segmentation of microscopy data. It is based on Segment Anything from Meta
In order to use the micro-sam toolkit it is recommended to use a computer with a decent GPU.
micro-sam can be use to interactively segment images (2D, 3D, time series) in napari. It can also be used to fine-tune the Segment Anything model to allow for automatic instance segmentation of your images.
Installation
It is advised to install micro-sam in a conda environment. Check here to install conda.
conda env create --file environment.yml -n micro-sam
conda install -c conda-forge micro_sam
To open the micro-sam plugins:
napari