Automating analysis with Fiji (ImageJ)

In this tutorial, we will focus on creating automated image processing pipelines with Fiji / ImageJ including 3D object segmentation, measuring intensity, and analyzing distance relationships. We will also cover additional plugins that extend the capability of Fiji for biomedical image analysis.

Ideal for those new to image analysis and scripting who want to batch process images. We start with building a simple macro and expand to automatically analyzing multi-channel datasets in a rigorous and reproducible manner. We also discuss ways of generating logs and recording results as well as useful shortcuts when using Fiji.

Data used in this workshop is available here: https://www.dropbox.com/sh/q3cl1favua...
Scripts created during this workshop are available here:
https://github.com/lahammond/CI_Image...

Recorded on Thursday, November 4, 2021, as part of Cellular Imaging's 2021 Image Analysis Program by Luke Hammond (Director of Cellular Imaging, Zuckerman Institute, Columbia University)

https://www.cellularimaging.org/

• #science_technology
• #imageanalysis
• #neuroscience
• #microscopy
• #imagej
• #fiji
• #image_analysis