Tool for Image Annotation and Training Cellpose

Graphical tool for quickly creating image segmentation annotations and training custom Cellpose models.

Main features:

1. Select regions of interests using Napari (from one or multiple images)
2. Create cell annotations using QuPath or Napari
3. Train a new Cellpose model (with the option to train your model via the browser using a remote server with GPU and CUDA support) or export the training data and train a new model using the cellpose>=2.0 interface.

To install it, see the documentation.

Features

Select regions of interests in Napari

Load one or more images (with one or multiple channels) and select the areas that you want to annotate and use for training.

Create annotations in QuPath or Napari

Get a QuPath project that you can directly use to annotate the regions you selected, or annotate them directly using Napari. Otherwise, you can also export the regions you selected in the format expected by the cellpose software and label them in cellpose

Train custom cellpose models

Train a new model directly from the tool, or export the training data and train a new model using the cellpose>=2.0 interface.

Train custom model on a remote server

If your machine does not have a GPU and CUDA support, you can install the TrainCellposeServer tool on a remote server with a GPU and train your models remotely via the browser (see Cellpose training server tool).