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napari-empanada-1.2

About

Empanada (EM Panoptic Any Dimension Annotation) is a tool for panoptic segmentation of organelles in electron microscopy (EM) images in 2D and 3D. Panoptic segmentation combines both instance and semantic segmentation enabling a holistic approach to image annotation with a single deep learning model.

Find further information at the official documentation of napari-empanada.

Requirements

  • Apptainer

Build Instructions

To build the container, run the following command in the terminal:

apptainer build napari-empanada-1.2.sif build.def

Run Instructions

This container runs by default napari with:

apptainer run napari-empanada-1.2.sif

[!IMPORTANT] Add the --nv flag to be able to use the GPU.

Notes

Known limitations

  • This application uses cztile==1.0.0 because latest version breake the app in our environment.
  • This is a RAM-hungry application. Depending on the site of your dataset, you may need to do some adjustmet for caching operations.

Feel free to rech out if your use-case requires specific configuration for this application.