Microscopy computational tools

This repository contains scripts to identify cell centers and obtain cell embeddings with pretrained machine learning models. The scripts can be run locally or on the Hail Batch service.

The scripts are easy to modify, e.g., to add a new model.

How to use

Start by using cellpose to identify cell centers. The output of the cellpose script can be used as input for the script that generates the embeddings.

Docker image

The Dockerfile in this folder can be used to create a Docker container with the scripts in this repository and all required dependencies. It supports both TIFF and JPEG-XL images. You could build the image by running the following commands on a Debian VM on GCP in the same folder as Dockerfile. You should replace PROJECT and REPOSITORY to point to your own artifact repository.

sudo apt update
sudo apt install docker.io
sudo usermod -a -G docker $USER
sudo su - $USER
docker build -t microscopy_computational_tools .
docker tag microscopy_computational_tools us-central1-docker.pkg.dev/PROJECT/REPOSITORY/microscopy_computational_tools
gcloud auth configure-docker us-central1-docker.pkg.dev
docker push us-central1-docker.pkg.dev/PROJECT/REPOSITORY/microscopy_computational_tools