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StuartLab / MiNA

MiNA (Mitochondrial Network Analysis) is a project aimed at making the analysis and characterization of mitochondrial network morphology more accurate, faster, and objective. This project currently consists of a set of Python scripts (and JAVA for the user interface) for the Fiji distribution of ImageJ.
GNU General Public License v3.0
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Output parameters #24

Open tierneyb opened 3 years ago

tierneyb commented 3 years ago

Hello!

I have successfully skeletonized the images and 2D/3D analyzed them to produce the ouput table in the screenshot attached.

It is then unclear to me how to show the nine parameters MiNA calculates from this table describing mitochondrial network morphology (as described in the paper). Our collaborators who have used the plugin before get a different parameter table that match those described in the paper - I am wondering if this has anything to do with the recent unicode bug. Hopefully you can help! Thanks! Screen Shot 2020-11-02 at 2 19 30 PM

Tierney

RodoVJ commented 3 years ago

Hi @tierneyb ! How are you running MiNA?

tierneyb commented 3 years ago

Hi RodoVJ,

I am running it as specified in Fig. 1 of the Valente et al., 2017 paper using ImageJ.

tierneyb commented 3 years ago
Screen Shot 2020-11-19 at 12 46 15 PM
RodoVJ commented 3 years ago

The two last columns are a description of what MiNA actually does for you. Also, which version are you using? I would advise you to use MiNA 3.0.0. You can go here MiNA and read the instructions on how to install and run the newest version of the tool.

Cheers, Rodrigo

tierneyb commented 3 years ago

Unless there has been an update since October 29th, I am running the latest version and downloaded according to the instructions you linked.

RodoVJ commented 3 years ago

There are instruction for running the tool under "Processing Pipeline and Usage". Are you able to open or see the main graphical interface of MiNA, where you are able to enter parameters and such?

snmzler commented 1 year ago

I have the same problem. I can see the output table atteched by @tierneyb above, but not the output table from MiNA. I'm running the latest MiNA version MiNA 3.0.1 and installed it according to the instructions given in GitHub. I can see the main graphical interface of MiNA, I can specify the paramaters. However, when I click to OK (or preview preprocessing), nothing happens (no overlay/ table and no error page). What could be the problem?

ahmtad commented 1 year ago

Hi,

I solved the problem by using an older version of MINA (2.0.0). I believe MINA needs an update to allow compatibility with new versions of FIJI.

1) Download the latest version of FIJI --> https://fiji.sc/ 2) Download MINA Analyze 2.0.0 --> https://github.com/StuartLab/MiNA/archive/refs/tags/2.0.0.zip 3) Follow the installation instructions: image