Introduction

A napari plugin for deep-learning based segmentation of cellular structures.


schematic of the input & output of Segmenter ML plugin

  • Available at no cost — available on PyPI

  • User-friendly — leverage napari as a fast 3D viewer with interactive plugin interface

  • Beginner-friendly — new to machine learning? This plugin simplifies the application of machine learning in the segmentation process through the 3 main modules:

    • Curation: curate training datasets

    • Training: iteratively train custom segmentation model(s) (UNET) to target cellular structure with wide morphological variability

    • Prediction & Thresholding: generate segmentation prediction on 2D and 3D cell image data


screenshot of napari with the Segmenter ML plugin

Segmenter ML plugin in napari viewer

About this User Guide

This document provides an overview of key concepts behind the plugin, offers step-by-step instructions for complete workflows, and share valuable resources, such as available pre-trained models (MegaSeg) and open-access training datasets.