Merge branch 'main' into main

faqs/galaxy/request-galaxy-tools-on-a-specific-server.md

@@ -8,8 +8,8 @@ contributors: [nomadscientist]
 ---
 To request tools that already exist in the [Galaxy toolshed](https://toolshed.g2.bx.psu.edu), but not in your server, please raise an issue at:
 
-- *Europe - usegalaxy.eu* | https://github.com/usegalaxy-eu/usegalaxy-eu-tools
+- *Europe - usegalaxy.eu* \| https://github.com/usegalaxy-eu/usegalaxy-eu-tools
 
-- *USA - usegalaxy.org* | https://github.com/galaxyproject/usegalaxy-tools
+- *USA - usegalaxy.org* \| https://github.com/galaxyproject/usegalaxy-tools
 
-- *Australia - usegaalxy.org.au* | https://github.com/usegalaxy-au/usegalaxy-au-tools/tree/master/usegalaxy.org.au
+- *Australia - usegaalxy.org.au* \| https://github.com/usegalaxy-au/usegalaxy-au-tools/tree/master/usegalaxy.org.au

news/_posts/2024-11-29-tracking-of-mitochondria-and-capturing-mitoflashes.md

@@ -0,0 +1,21 @@
+---
+title: "New Tutorial: Tracking of mitochondria and capturing mitoflashes"
+layout: news
+tags:
+- bioimaging
+- mitoflash
+- mitochondria
+contributions:
+  authorship:
+  - dianichj
+  - kostrykin
+cover: "topics/imaging/images/detection-of-mitoflashes/Workflow_mitoflash.png"
+coveralt: "Analysis Pipeline for Tracking Mitochonria and Capturing Mitoflashes."
+tutorial: topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html
+---
+
+We are happy to share that a new imaging tutorial for **Tracking Mitochondria and Capturing Mitoflashes** is now available in the Galaxy Training Network!
+
+![Mitoflash Analysis Pipeline]({% link topics/imaging/images/detection-of-mitoflashes/Workflow_mitoflash.png %} "Analysis Pipeline for Tracking Mitochonria and Capturing Mitoflashes. Overview of the workflow for detecting mitoflash using Mitochondrion detection (Step 1), Mitochondrion tracking (Step 2), and Curve fitting to measured intensities (Step 3).")
+
+This tutorial, Tracking of mitochondria and capturing mitoflashes, provides a step-by-step guide on analyzing mitoflash events in mitochondria using Galaxy. Mitoflashes are transient mitochondrial events characterized by bursts of reactive oxygen species (ROS), membrane potential depolarization, and matrix alkalinization. They are linked to bioenergetic states, physiological processes (like muscle contraction and neuronal development), and may serve as markers of mitochondrial health and longevity. Our tutorial explains how to preprocess imaging data, identify mitoflash events, and quantify key parameters (amplitude, duration, and frequency) using informatics tools in Galaxy. It is designed for researchers studying mitochondrial behavior in health and disease.

topics/galaxy-interface/tutorials/history-to-workflow/tutorial.md

@@ -54,7 +54,7 @@ This practical shows how to create a reusable analysis pipeline, called a *workf
 > 1. An internet-connected computer.  Galaxy can run on your laptop without an internet connection, but this practical requires access to resources on the web.
 > 1. A web browser. [Firefox](https://www.mozilla.org/firefox) and [Google Chrome](https://www.google.com/chrome/) work well, as does [Safari](https://www.apple.com/safari/).  Internet Explorer is known to have issues with Galaxy so avoid using that.
 > 1. Access to a Galaxy instance, and an account on that instance. Galaxy is available in many ways. If you are doing this practical as part of a workshop, the instructor will tell you which instance to use. If you are doing this on your own, you can use [usegalaxy.org](https://usegalaxy.org).
-> 1. A Galaxy *history* from an analysis that you have already run.  If you don't have one handy, you can use [this history](https://usegalaxy.org/u/tnabtaf/h/overlapping-genes-on-opposite-strands). on usegalaxy.org.  Click **Import History** (top right) to bring that history into your workspace on usegalaxy.org. Any history will work with this tutorial, but that's the one used in the examples.
+> 1. A Galaxy *history* from an analysis that you have already run.  If you don't have one handy, you can use [this history](https://usegalaxy.org/u/tnabtaf/h/overlapping-genes-on-opposite-strands-1). on usegalaxy.org.  Click **Import History** (top right) to bring that history into your workspace on usegalaxy.org. Any history will work with this tutorial, but that's the one used in the examples.
 {: .comment}
 
 This tutorial is a good second step after running your first analysis on Galaxy.