cell-AAP 1.0.2

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Cellular Annotation & Perception Pipeline

Description

Cell-APP automates the generation of cell masks (and classifications too!), enabling users to create custom instance segmentation training datasets in transmitted-light microscopy. To learn more, read our preprint: https://www.biorxiv.org/content/10.1101/2025.01.23.634498v2.

Usage

1. Users who wish to segment HeLa, U2OS, HT1080, or RPE-1 cell lines may try our pre-trained model. These models can be used through our GUI (see Installation) and their weights can be downloaded at: https://zenodo.org/communities/cellapp/records?q=&l=list&p=1&s=10. To learn about using pre-trained models through the GUI, see this video:

2. Users who wish to segment their own cell lines may: (a) try our "general" model (GUI/weight download) or (b) train a custom model by creating an instance segmentation dataset via our Dataset Generation GUI (see Installation). To learn about creating custom datasets through the GUI, see this video:

Installation

We highly recommend installing cell-APP in a clean conda environment. To do so, you must have miniconda or anaconda installed.

Once a conda distribution has been installed:

1. Create and activate a clean environment

    conda create -n cell-aap-env python=3.11.0
    conda activate cell-app-env
   

2. Within this environment, install pip

    conda install pip
   

3. Then install the package from PyPi (the package bears the name "cell-AAP;" a historical quirk)

    pip install cell-AAP --upgrade
   

4. Finally detectron2 must be built from source, atop cell-AAP

    #For MacOS
    CC=clang CXX=clang++ ARCHFLAGS="-arch arm64" python -m pip install 'git+https://github.com/facebookresearch/detectron2.git'
   
    #For other operating systems 
    python -m pip install 'git+https://github.com/facebookresearch/detectron2.git'
   

Napari Plugin Usage

1. To open napari simply type "napari" into the command line, ensure that you are working the correct environment
2. To instantiate the plugin, navigate to the "Plugins" menu and hover over "cell-AAP"
3. You should see three plugin options; two relate to Usage 1; one relates to Usage 2.