3D Mitochondria Analysis Using ImageJ: (Part1)

Join me in this tutorial as I dive into the fascinating world of mitochondria and explore the power of ImageJ, an open-source image processing program designed for scientific multi-dimensional images.
In this video, I will guide you through analyzing various aspects of 3D mitochondrial images. You will learn how to obtain information such as mitochondria distribution, proximity to each other, and much more.
This analysis will help you to understand a wealth of information and allow you to characterize the behavior and characteristics of mitochondria in 3D space.
I will walk you through the steps of Using the “Mitochondria Analyzer,” a plugin for ImageJ, and show you how to convert your images to 8-bit, set the scale to microns, and threshold your images. You will also learn how to visually check the quality of your threshold and view your thresholded image in 3D.
This tutorial will also cover measuring distances between objects and analyzing your mitochondria through the 3D analysis option on the Mitochondria Analyzer and the 3D Manager. You will learn how to calculate various ratios and understand the shape of your mitochondria.
Stay tuned for my next video, in which I will show you how to use a Jupyter script to take all of this data and utilize it in another fashion for k-means clustering.
ImageJ Plugin: Mitochondria Analyzer - github.com/Ahs...
ImageJ (FIJI): imagej.net/sof...
Deconvolution Lab 2: (For those looking to use deconvolution) - bigwww.epfl.ch...

[@MrUnis]

Hi, amazing tutorial....i am trying to do mitoanalysis but i am getting an error, unrecognized command Sigma filter plus in line 194...Could you help me here please?
if (canSigma) run("Sigma Filter Plus", "radius=" + sRadius + " use=2.0 minimum=0.2 outlier stack"..................why for thresholding in 3D, it does not recognize this command.

[@NeuroGuides]

Please make sure that you are running MitochondrialAnalyzer from FIJI distribution of ImageJ (fiji.sc/). Try re-installing the sigma filter plus (imagej.net/ij/plugins/sigma-filter.html). In addition, please make sure that you have 3D ImageJ Suite, ImageScience, IJPB-Plugins (with MorphoLibJ) by going to FIJI tab: Help -> Update…. -> Manage Update Sites -> check 3D ImageJ Suit, ImageScience, IJPB-Plugins.

[@da-avdymensobsession2346]

Hi your tutorial is good you did not uploaded next part

[@NeuroGuides]

😅 Just posted it with updates. Thanks for reminding me. Here's the link: th-cam.com/video/Bm_Se4pPFtA/w-d-xo.html