Skip to content

Home

Jump to bottom
António Brito edited this page Aug 5, 2025 · 1 revision

Welcome to the napari-mAIcrobe wiki!

What is napari-mAIcrobe

napari-mAIcrobe is a napari plugin that was developed for the semi-automated analysis bacterial fluorescence microscopy images. The focus of napari-mAIcrobe is to offer an easy-to-use and accessible interface for bacterial image analysis. It tries its best at being agnostic regarding the bacterial species and microscopy modality.

Currently implemented features:

  • Instance segmentation using a variety of traditional and deep-learning approaches (thresholding, StarDist models, CellPose models, bespoke U-Net models etc)
  • Computation of a variety of morphological and fluorescence metrics
  • Instance classification

napari-mAIcrobe is the spiritual sucessor of eHooke.

Clone this wiki locally