Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/rocsg/rootsystemtracker


https://github.com/rocsg/rootsystemtracker

Last synced: about 2 months ago
JSON representation

Awesome Lists containing this project

README 

        
RootSystemTracker README

*************************



Welcome to RootSystemTracker github.



* More informations about RootSystemTracker : 

https//imagej.net/rootsystemtracker



Current version : Handsome Honeysuckle (last release : July 13th, 2022).



The plugin **RootSystemTracker** is an automatic analysis pipeline based on registration and topological tracking, capable of accurately describing the topology and geometry of observed root systems in 2D+t.



## Plugin features



-   2D segmentation of time series with root apparition time

-   Reconstruction of Root System Architecture

-   Movie Builder (interpolated growth of the root system, see below)

-   High-throughput (automatic batch processing)



## Preparing your dataset



**Input data:** 2D + t image sequence acquired with an imaging automaton presenting a growing root system in a petri dish. Data should be organized in an input directory, one subdirectory per dish, with name patterning such as img_XX.tif, in order that ImageJ detect the image sequence autonomously.



**Output data:** 2D segmentation with root apparition time, root skeleton, root system architecture as a RSML file, and an interpolated movie of the growing root system (see below)



## Demo



The following video shows the movie produced by RootSystemTracker on a specimen



https://www.youtube.com/watch?v=SWEqnnOhIOU



## Installation



In order to install RootSystemTracker on your computer, please follow these simple steps:



1\. (if needed) Download and install Fiji from https://fiji.sc/ ; start Fiji, and let it automatically update. Then restart Fiji.



2\. Open Fiji, run the **Update manager** {% include bc path="Help | Update" %}. Click on "OK" to close the first popup windows, then click on the button **Manage update sites...**.



3\. In this list, activate **ImageJ-ITK** and **IJPB-plugins** by checking the corresponding checkboxes.



and add the **Fijiyama** repository (by clicking on the button **Add update site**, and filling the fields : name = "/plugins/fijiyama", site = https://sites.imagej.net/Fijiyama), then check the associated checkbox.



4\. Restart Fiji: a new **RootSystemTracker** entry should be available in the menu {% include bc path="Plugins | Analyze" %}. If not, go back to the Update Manager, and check that the repositories **ImageJ-ITK**, **IJPB** and **Fijiyama** are correctly selected.



The following video shows a tutorial for Fijiyama and RootSystemTracker installation:



{% include video platform='youtube' id='scm6UPlfgzU'%}



## Running the plugin



Open Fiji, then click on {% include bc path="Plugins | Analyze | Root System Tracker" %}

When prompted, identify the input then output path. The plugin then prompt you to edit the parameter file if needed, then run autonomously.



## Versions of RootSystemTracker



It is a living project, with frequent updates. Thanks to the Fiji updater, your version is updated each time the Fiji update starts.



Major updates include new features released, or major refactoring, while minor updates (change in the release time) should not modify deeply the behaviour of the plugin, to keep results reproducible. These information can be seen in the launching interface.



## Citing this work



-  Romain Fernandez, Amandine Crabos, Morgan Maillard, Philippe Nacry, Christophe Pradal. High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings. bioRxiv 2022.07.13.499903; doi: https://doi.org/10.1101/2022.07.13.499903



## Contact



Issues, feature request ? Please contact romainfernandez06ATgmail.com