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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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MiNA plugin not working #54

Open MeenakshiM26 opened 1 year ago

MeenakshiM26 commented 1 year ago
Screenshot 2023-05-22 at 6 04 44 PM Screenshot 2023-05-22 at 6 22 32 PM Screenshot 2023-05-22 at 6 26 44 PM

Hi, I have added the Mina plugin as suggested by Alex H.

Installation You should have FIJI 35 installed.

  1. Download the contents of this repository as a zipped folder
  2. Go to your FIJI installation and go to the “Fiji.app” folder. If you’re using mac, right click on the FIJI icon and select “Show Package Contents”.
  3. Move the folder with the name “mina” located in “src” of this repository to jars>Lib (create the folder Lib if it does not already exist).
  4. Move the file “MiNA_Analyze_Morphology.py” located at “src>scripts” to “scripts”.
  5. Move the folder “mina_icons” inside “images”.
  6. In the “build” folder of this repository you will see a jar file. Move it inside “plugins”.
  7. Finally, start ImageJ and if you don’t have the Biomedroup site installed then click on Help->Update… Navigate to the update site manager (Manage update sites). Add the “Biomedgroup” site by checking the checkbox beside the site. Close the site manager dialog (Close) and apply the changes (Apply changes).

however, after installation when I am running the plugin, it is not working (screenshot attached). Kindly help.

Rayanu commented 1 year ago

Hello, I actually have the same issue and I don't know how to solve it. If you found a solution i would appreciate if you shared it

MeenakshiM26 commented 1 year ago

Hi, I was struggling with two steps. Step 5. I was mistakenly transferring the entire MiNA folder into the "image" folder. I have corrected it and transferred only "mina_icon" inside images. Step 7. While updating the site manager and adding "Biomedgroup", I was also adding Stuart Lab. I think that was causing some interference or issues. This confusion occurred as I have followed installation suggestions from Wikipedia before. This time, I only selected "Biomedgroup" and it worked. I wish someone could update the installation manual available on wiki. It could have saved so much time and effort. Hope this might be helpful. Best, Meenakshi

giampierolago commented 1 year ago

I have the same issue; I've do what you advise in this post but the solution not working for me (both on a Mac and a Windows computer); this is the output:

(Fiji Is Just) ImageJ 2.9.0/1.54e; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 71MB of 5844MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:308) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:152) at ij.Executer.run(Executer.java:70) at java.lang.Thread.run(Thread.java:750) Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304) ... 5 more Caused by: java.lang.RuntimeException: Module threw exception at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: java.lang.ClassCastException: java.lang.Double cannot be cast to java.math.BigInteger at org.scijava.ui.swing.widget.SpinnerNumberModelFactory.createModel(SpinnerNumberModelFactory.java:56) at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:123) at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:74) at org.scijava.plugin.WrapperService.create(WrapperService.java:65) at org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:110) at org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:84) at org.scijava.widget.InputHarvester.harvest(InputHarvester.java:67) at org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:74) at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:152) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124) ... 6 more

Thanks Giampiero

fsangalli72 commented 11 months ago

Hi, I also tried the previously written solution but it doesn't work, does anyone have any ideas?

nahow97 commented 11 months ago

Hi, I am having a similar issue. I cannot add the Stuart Lab and Biomed plug ins in my Image J download. I am using a Mac and every time I put update link it closes the application and doesn't have the option to add plug-ins.

Could you help me please?

Thank you

zelunw commented 10 months ago

Check out this pull request. Changing BigInteger to Integer in MiNA_Analyze_Morphology.py worked for me