FIJI (ImageJ): Morphology & Network Analysis of Mitochondria

Learn how to use FIJI (ImageJ) to analyze fluorescent 2D, 3D (z-stacks) and time-lapse images of mitochondria. This tutorial demonstrates the use of the plugin called Mitochondria Analyzer, which showcases a semi-automated pipeline of image pre-processing, object detection by adaptive or local thresholding, post-processing, and extraction of morphological and network characteristics of mitochondria. The plugin also has the ability to combine morphological or networking with functional analysis through simultaneous intensiometric measurements of co-stained mitochondrial reporters, allowing for “morpho-functional” measurement of mitochondria. Automatic batch thresholding and analysis can also be done. Chapter timeline: 0:00 Introduction 0:37 Mitochondria Analyzer pipeline for 2D images 5:04 Analysis Pipeline for 3D (z stack) images 7:10 Analysis Pipeline for time lapse images 9:26 Batch analysis Installation instructions and detailed manual: https://github.com/AhsenChaudhry/Mito... ***URL to add to Fiji update sites: http://sites.imagej.net/ACMito/ Plugin citation: Chaudhry A, Shi R, Luciani DS. A Pipeline for Multidimensional Confocal Analysis of Mitochondrial Morphology, Function, and Dynamics in Pancreatic β-cells. Am J Physiology-Endocrinology Metab (2020) 318:E87–E101. doi:10.1152/ajpendo.00457.2019 Image citation: z-stack: Brenda Kostelecky (2011) CIL:11933, Rattus. CIL. Dataset. https://doi.org/doi:10.7295/W9CIL11933 timelapse image: Kasturi Mitra (2011) CIL:9070, Rattus, fibroblast. CIL. Dataset. https://doi.org/doi:10.7295/W9CIL9070 SUBSCRIBE to have first access to new video tutorials:    / @johanna.m.dela-cruz