Nucleolus Segmentation

A specialized image segmentation tool for nucleolus analysis, developed during my time at Weber Lab at McGill University. This repository is built on the basis of AllenCell segmenter (Classic Image Segmentation).

Goals:

1. Segments the nucleolus with markers of granular component (GC).

2. Characterizes features of nucleoli: size, number, and shape.

3. Analyzes the correlation between different nucleolar proteins within the nucleolar mask.

Installation

Prerequisites

• Python 3.9
• Anaconda (recommended)

Step 1: Install aics-segmentation

1. Visit the aics-segmentation repository
2. Follow the official installation guide

Step 2: Install nucleolus_segmentation_public

1. Clone the repository:

   cd C:\Projects
   git clone https://github.com/ashapeng/nucleolus_segmentation_public.git

   Alternatively, download the ZIP file and extract it to your project folder.

2. Install required packages:

   cd C:\Projects\nucleolus_segmentation_public
   pip install -r installer.txt

Visualization Tools

For visualization, you have two options:

1. itkwidgets: Follow the AllenCell's help guide
2. napari (recommended): More stable alternative. Installation instructions available at napari.org

3.Run this repository:

• 3.1: Unzip test_image folder: this will be the data used for running this repository.

• 3.2. Run nucleolus_seg.ipynb: to test segmentation with one example image, then run batch mode to process folders

• 3.3. Run nucleolus_feature_descriptor.ipynb or intensity based analysis, after save nucleolar mask in 3.2