Image Analysis

There are two main image analysis software programs in neuroscience, namely ImageJ and Cell Profiler, both of which are free, open-source, and have a large community of users.

Table of Contents

• Image Analysis
  • ImageJ
    • Fiji
  • Cell Profiler

ImageJ

ImageJ is a Java image processing and analysis program.

• Wiki
• User Guide

Fiji

Fiji is an ImageJ distribution with built-in plugins. It is the recommended way to use ImageJ.

Note

ImageJ commands can be integrated into Python code. To see how, check out the materials from the ImageJ Macro Workshop hosted by NINC during the 2019 MSC-SMC Annual Meeting at UBC.

Cell Profiler

Cell Profiler is a cell image analysis software that enables users to construct pipelines for cell identification and measurement of phenotypes including morphology, intensity, texture, and size.