stuartlab / mina Goto Github PK

when i click "Analyze",alert this mistakes

When attempting top drag the mina folder over to the Fiji.app, I receive an error stating that the file is corrupt.

After seeing the same errors that some other users have reported, I downloaded a 2017 version of FIJI from its official site. The program ran better on that version (with some errors that still need to be ironed out). I would suspect that this means MiNA needs to be updated for the latest version of FIJI.

Kindly help. A detailed step-by-step procedure to rectify the error will be helpful as I have zero programing or debugging knowlegde.

[INFO] Reading available sites from https://imagej.net/
[INFO] Reading available sites from https://imagej.net/
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
[ERROR] Traceback (most recent call last):
File "MiNA_Analyze_Morphology.py", line 20, in
ImportError: No module named eztables

Hi, I noticed that MiNA no longer outputs "individual" and "network" in the new version. May I know the reason behind this change? Also, what values in the new output can help me determine the ratio of fission and fusion mitochondria?

Thanks!

Hello,

I have been trying to run MiNa but keep getting an Exception file (see attachment). I have reinstalled MiNa (including the updates from this site) and added Biomedroup/Stuartlab but am having no luck. I have also asked a colleague to take a look and they too cannot get MiNa to run. Can someone have a look please? Thanks. Rachel
miNA.docx
el

While running an analysis, the median branches values was always found to be 1. Let's double check that this is being computed correctly, both in the branch count and determining the median.

• Verify the branch counts variable contents match AnalyzeSkeleton's table output.
• Verify that the median is correctly calculated.

Hi, I noticed that on converting the binary image to Skelton it is always white skeleton against a black background.
could you please help to fix that.

Thank you
hanan

Hi, I have tried to run both versions of MiNA but after clicking run I got this macro error message:

statement cannot beging with '<' in line 7.
!DOCTYPE html

Thank you!

Hello, i am trying MiNa through Fiji. I installed everything following the installation guide. I also tried updating Fiji. I always get the same Error (see the console log below). It is not clear to me how to get that missing module, i don't have pip in this computer (and i doubt i could install it), but i don't think it would work anyway.

[ERROR] null
Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: No module named eztables

at org.python.core.Py.ImportError(Py.java:334)
at org.python.core.imp.import_first(imp.java:879)
at org.python.core.imp.import_module_level(imp.java:964)
at org.python.core.imp.importName(imp.java:1057)
at org.python.core.ImportFunction.__call__(__builtin__.java:1280)
at org.python.core.PyObject.__call__(PyObject.java:450)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1076)
at org.python.pycode._pyx6.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx6.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Hi,

great tool! Does anyone have a macro for processing multiple images?

Kind regards,
Johannes

Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: java.io.FileNotFoundException: C:\Users\TARUN\Desktop\ICON\fiji-win64\Fiji.app\scripts\MiNA_Analyze_Morphology.py (The system cannot find the file specified)
at org.scijava.script.ScriptInfo.parseParameters(ScriptInfo.java:294)
at org.scijava.module.AbstractModuleInfo.initParameters(AbstractModuleInfo.java:189)
at org.scijava.module.AbstractModuleInfo.inputMap(AbstractModuleInfo.java:139)
at org.scijava.module.AbstractModuleInfo.getInput(AbstractModuleInfo.java:73)
at org.scijava.module.DefaultModuleService.assignInputs(DefaultModuleService.java:456)
at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:239)
at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:208)
at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:189)
at org.scijava.script.DefaultScriptService.run(DefaultScriptService.java:187)
at org.scijava.script.DefaultScriptService.run(DefaultScriptService.java:173)
at MiNAgui.runMiNA(MiNAgui.java:126)
at MiNAgui.lambda$run$4(MiNAgui.java:233)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.io.FileNotFoundException: C:\Users\TARUN\Desktop\ICON\fiji-win64\Fiji.app\scripts\MiNA_Analyze_Morphology.py (The system cannot find the file specified)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at org.scijava.script.process.ScriptProcessorService.process(ScriptProcessorService.java:62)
at org.scijava.script.ScriptInfo.parseParameters(ScriptInfo.java:290)
... 47 more
[INFO] Reading available sites from https://imagej.net/
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: java.io.FileNotFoundException: C:\Users\TARUN\Desktop\ICON\fiji-win64\Fiji.app\scripts\MiNA_Analyze_Morphology.py (The system cannot find the file specified)
at org.scijava.script.ScriptInfo.parseParameters(ScriptInfo.java:294)
at org.scijava.module.AbstractModuleInfo.initParameters(AbstractModuleInfo.java:189)
at org.scijava.module.AbstractModuleInfo.inputMap(AbstractModuleInfo.java:139)
at org.scijava.module.AbstractModuleInfo.getInput(AbstractModuleInfo.java:73)
at org.scijava.module.DefaultModuleService.assignInputs(DefaultModuleService.java:456)
at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:239)
at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:208)
at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:189)
at org.scijava.script.DefaultScriptService.run(DefaultScriptService.java:187)
at org.scijava.script.DefaultScriptService.run(DefaultScriptService.java:173)
at MiNAgui.runMiNA(MiNAgui.java:126)
at MiNAgui.lambda$run$3(MiNAgui.java:205)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.io.FileNotFoundException: C:\Users\TARUN\Desktop\ICON\fiji-win64\Fiji.app\scripts\MiNA_Analyze_Morphology.py (The system cannot find the file specified)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at org.scijava.script.process.ScriptProcessorService.process(ScriptProcessorService.java:62)
at org.scijava.script.ScriptInfo.parseParameters(ScriptInfo.java:290)
... 47 more

Hi, I reinstalled FIJI, installed the newest MiNA 3.0 based on Readme instruction on my macbook.
My workflow is: open TIFF image, change it to 8bit file, filters->unsharp mask, CLAHE, plugins->Stuartlab->MiNA Analyze Morphology, after clicking "OK", the error will popup as:

3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily
/Users/Devin_Xu/.ImageJ_3D_Viewer.props (No such file or directory)
[ERROR] Traceback (most recent call last):
File "/Applications/Fiji.app/scripts/MiNA_Analyze_Morphology.py", line 273, in
run(imp, preprocessor_path, postprocessor_path, threshold_method, user_comment)
File "/Applications/Fiji.app/scripts/MiNA_Analyze_Morphology.py", line 242, in run
morphology_tbl.writeRow(output_parameters, mina.tables.commentToDict(user_comment))
File "/Applications/Fiji.app/jars/Lib/mina/tables/_simplesheet.py", line 57, in writeRow
self.rt.addValue(key, str(value))
UnicodeEncodeError: 'ascii' codec can't encode characters in position 13-16: ordinal not in range(128)

at org.python.core.codecs.strict_errors(codecs.java:206)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.python.core.JavaFunc.__call__(Py.java:2895)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.codecs.encoding_error(codecs.java:1537)
at org.python.core.codecs.PyUnicode_EncodeIntLimited(codecs.java:1210)
at org.python.core.codecs.PyUnicode_EncodeASCII(codecs.java:1169)
at org.python.core.codecs.encode(codecs.java:163)
at org.python.core.PyString.encode(PyString.java:3995)
at org.python.core.PyString.encode(PyString.java:3987)
at org.python.core.PyUnicode.unicode___str__(PyUnicode.java:681)
at org.python.core.PyUnicode.__str__(PyUnicode.java:676)
at org.python.core.PyString.str_new(PyString.java:172)
at org.python.core.PyString$exposed___new__.new_impl(Unknown Source)
at org.python.core.PyType.invokeNew(PyType.java:1119)
at org.python.core.PyType.type___call__(PyType.java:2399)
at org.python.core.PyType.__call__(PyType.java:2389)
at org.python.core.PyObject.__call__(PyObject.java:461)
at org.python.core.PyObject.__call__(PyObject.java:465)
at mina.tables._simplesheet$py.writeRow$3(/Applications/Fiji.app/jars/Lib/mina/tables/_simplesheet.py:52)
at mina.tables._simplesheet$py.call_function(/Applications/Fiji.app/jars/Lib/mina/tables/_simplesheet.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyBaseCode.call(PyBaseCode.java:306)
at org.python.core.PyBaseCode.call(PyBaseCode.java:158)
at org.python.core.PyFunction.__call__(PyFunction.java:437)
at org.python.core.PyMethod.__call__(PyMethod.java:156)
at org.python.pycode._pyx1.run$8(/Applications/Fiji.app/scripts/MiNA_Analyze_Morphology.py:263)
at org.python.pycode._pyx1.call_function(/Applications/Fiji.app/scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyBaseCode.call(PyBaseCode.java:306)
at org.python.core.PyFunction.function___call__(PyFunction.java:474)
at org.python.core.PyFunction.__call__(PyFunction.java:469)
at org.python.core.PyFunction.__call__(PyFunction.java:459)
at org.python.pycode._pyx1.f$0(/Applications/Fiji.app/scripts/MiNA_Analyze_Morphology.py:273)
at org.python.pycode._pyx1.call_function(/Applications/Fiji.app/scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

How do we decide the parameter after selecting ridge detection?
Given manual / image J wiki asked to select ridge detection for 2D images. However, I am not clear on what basis and how we decide the input of those parameters.
Please guide.
Thank you in advance

Dear all,
I install the last version of Fiji, Stuart lab and Biomedgroup and I tried Mina on 2 PC.
I deleted the file in question: Fiji.app/jars/Lib/eztables/init$py.class and other $py.class files in that folder.
But I always have the same issue.
Could you help me ?

Kind regards,

Hi all
previously i already had MiNA plugin running on my fiji;
however i wanted to update the latest verison of the plugin and
i followed the installation steps of the plugin according to this repo

however;
when i run MiNA
i get this output on command log

File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Users\k\Downloads\fiji-win64\Fiji.app\jars\Lib\eztables_init_$py.class

may i know how do i resolve this?

Hi,
I downloaded new version and installed the plugin as in read me document.
When i start the plugin, MiNA Analyze Morphology window opens up.
I choose a file for pre processor path and post processing path and select preprocessing option and thresholding option and hit ok. It errors out an opens same image that is already opened in Fiji.

Also is it necessary to open an image on Fiji before entering information on pre processing path.

Any help would be appreciated.
Thank you

Is it possible to select a cell with the freehand selection tool instead of the rectangular ROI tool? I would benefit from using freehand selection because with rectangular selection I often cannot exclude other cells from the selection. @RodoVJ

I got this:
javax.imageio.IIOException: Can't read input file!
at javax.imageio.ImageIO.read(ImageIO.java:1302)
at MiNAgui.run(MiNAgui.java:246)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
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)
at java.lang.Thread.run(Thread.java:750)

How to solve it?!

I had worked with the previous updates of the Mina and the Tophat algorithm was the one who always achieved the best result in mapping the mitochondria. I do not seem to find this option in the newer versions. Is this option available?
Thank you!

Hello

Received the following error while trying to run MiNA Analyze Morphology via Fiji on a new Windows 10 AIO Desktop:

console: Failed to install ": java.nio.charset.UnsupportedCharsetException: cp0
3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily

Latest version of Fij/ImageJ being used. All plugins and updates installed as detailed in the MiNa Wiki: https://imagej.net/MiNA_-_Mitochondrial_Network_Analysis

MiNa and related plugins work fine on my two other computers (both with dedicated nvidia GPUs). New desktop is running a i7-9700 with Intel integrated graphics (Intel Uhd 630 graphics driver).

Do you have any information or fixes concerning these two error messages?

Many Thanks,

Richard

Hi!
I have an issue with Mina plugin. I get the error that was reported before, but none of the answers help me. I have tried updating Fiji, uninstalling it, removing the plugins, but nothing helps.
Any idea? It used to work on my laptop and work computer, but now i can't run it on any computer at work.

When I run the plugin following analyse skeleton the output looks fine with regards to Mito Footprint and Branch Length mean however, network branches mean always comes back as 0 or 1. Is this running correctly and is this the value I should expect?

The default skeleton image is in the top left corner of the original image and can only be saved by means of a screenshot. However, the resolution of the saved image is too low, so I want to save the skeleton image as a separate image.thank you,look forward to your reply!

Hi,

I am having issues on both Windows and a Mac, running the StuartLab-> MiNA Script -> MiNA Analyze Morphology Plug-in. An exception window comes up and says the following:

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 51MB of 5930MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:150)
at ij.Executer.run(Executer.java:68)
at java.lang.Thread.run(Thread.java:748)
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:303)
... 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.NullPointerException
at org.scijava.ui.swing.widget.SwingNumberWidget.lambda$suitableFormat$0(SwingNumberWidget.java:344)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.reduce(ReferencePipeline.java:479)
at java.util.stream.ReferencePipeline.max(ReferencePipeline.java:515)
at org.scijava.ui.swing.widget.SwingNumberWidget.suitableFormat(SwingNumberWidget.java:344)
at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:127)
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

I keep seeing "Module threw exception" and was wondering what I could do. I have tried uninstalling and installing Fiji and also updated Java to the latest version. Would appreciate any help or advice!

Hi,

I am once more getting the error:

_[ERROR] Traceback (most recent call last):

File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required)._

I've reinstalled MiNa from the Master, and added Biomedroup / Stuartlab to the update sites. Any suggestions? Cheers.

Updated FIJI today, and the plugin won't run
[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required)

Hi
On running the plugin ( MINA analyze morphology ) tool I received the following message :

(3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily

C:\Users\SPECTRE.ImageJ_3D_Viewer.props (The system cannot find the file specified)

Hi all;

the network branch median is always 1 in my case when i execute MiNA plugin
may I know how to resolve this and is this normal?

my macro is below:
run("Unsharp Mask...", "radius=2 mask=0.60"); run("Enhance Local Contrast (CLAHE)", "blocksize=127 histogram=256 maximum=3 mask=*None*"); run("Median...", "radius=1"); setOption("BlackBackground", false); run("Make Binary"); run("Duplicate...", " "); run("Skeletonize");

after executing the preprocessing macro;
i clicked plugins>> stuart lab>>MiNA mitochondria morphology

ridge selection is selected and i get the following output

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!

Tierney

(Fiji Is Just) ImageJ 2.9.0/1.53t; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 56MB of 5235MB (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
(Fiji Is Just) ImageJ 2.9.0/1.53t; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 56MB of 5235MB (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

I have MiNA updated and have tried uninstalling fiji and reinstalling however when I run StuartLab-->MiNA Script -->MiNA Analyze Morphology I keep getting an IndexError: index out of range:1 (see below). I had been using it successfully for 2 hours before that point, now however, it is no longer working. Any advice would be appreciated.

Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 291, in
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 213, in run
IndexError: index out of range: 1

at org.python.core.Py.IndexError(Py.java:280)
at org.python.core.SequenceIndexDelegate.checkIdxAndGetItem(SequenceIndexDelegate.java:63)
at org.python.core.PySequence.seq___getitem__(PySequence.java:377)
at org.python.core.PySequence.__getitem__(PySequence.java:373)
at org.python.pycode._pyx0.run$2(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:287)
at org.python.pycode._pyx0.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:308)
at org.python.core.PyFunction.function___call__(PyFunction.java:471)
at org.python.core.PyFunction.__call__(PyFunction.java:466)
at org.python.core.PyFunction.__call__(PyFunction.java:456)
at org.python.pycode._pyx0.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx0.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

When trying to use the plugin, I keep getting this error:

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Users\zainh\AppData\Local\Temp\Rar$EXa11036.12434\Fiji.app\jars\Lib\eztables_init_$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx0.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx0.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

This has happened on two separate devices I've attempted to use this on. Any suggestions on how to fix this? Thanks!

Hi,
I hope you are all well,
I installed all the parts of MiNA as you kindly explained in read.me section. When I tried to run it gave me a warning saying 'ImagePlus is required but none exists'.
I googled but could not find how to include it in MiNA,
Many thanks for helping in advance,

Installation through the update manager on a fresh Fiji installation in Windows 7 results in an incomplete user interface and issues finding the eztables.statistical module.

Error Message:

File "C:\Users\user\Fiji.app\plugins\Scripts\Plugins\StuartLab\MiNA_Scripts\MiNA_Analyze_Morphology.py", line 20, in <module>  import eztables.statistical
ImportError: No module named statistical"

User Interface Screenshot:

I'm trying to get MiNA to work but am having some issues. I made the mistake of initially installing it via Update, but I removed StuartLab from Update and installed using instructions and the file from GitHub. This was an improvement since I could now at least open MiNA. When I click OK with an image open and an ROI selected, I get the error below.

I am going to guess that something is messed up from when I initially installed it, but hopefully someone can shed some light on this.

Thanks,

CKT

[ERROR] Traceback (most recent call last):
File "C:\fiji-win64\Fiji.app\scripts\MiNA_Analyze_Morphology.py", line 41, in
import mina.statistics
ImportError: No module named mina

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.import_first(imp.java:1230)
at org.python.core.imp.import_module_level(imp.java:1361)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx1.f$0(C:/fiji-win64/Fiji.app/scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx1.call_function(C:/fiji-win64/Fiji.app/scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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.

I recently downloaded and used the MiNA plug in successfully. However today every time I try to use it I get the following error message. I have tried uninstalling it and re-installing and this did not help.

ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 291, in
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 136, in run
at net.imglib2.histogram.Real1dBinMapper.min(Real1dBinMapper.java:237)
at net.imglib2.histogram.Real1dBinMapper.center(Real1dBinMapper.java:265)
at net.imglib2.histogram.Real1dBinMapper.getCenterValue(Real1dBinMapper.java:151)
at net.imglib2.histogram.Real1dBinMapper.getCenterValue(Real1dBinMapper.java:49)
at net.imglib2.histogram.Histogram1d.getCenterValue(Histogram1d.java:300)
at net.imagej.ops.threshold.AbstractComputeThresholdHistogram.compute(AbstractComputeThresholdHistogram.java:53)
at net.imagej.ops.threshold.AbstractComputeThresholdHistogram.compute(AbstractComputeThresholdHistogram.java:41)
at net.imagej.ops.threshold.ApplyThresholdMethod$IsoData.getThreshold(ApplyThresholdMethod.java:155)
at net.imagej.ops.threshold.ApplyThresholdMethod$IsoData.getThreshold(ApplyThresholdMethod.java:134)
at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:52)
at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:43)
at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:136)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: invalid bin position specified

at org.python.core.Py.JavaError(Py.java:552)
at org.python.core.Py.JavaError(Py.java:543)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:206)
at org.python.core.PyObject.__call__(PyObject.java:515)
at org.python.core.PyObject.__call__(PyObject.java:519)
at org.python.core.PyMethod.__call__(PyMethod.java:156)
at org.python.pycode._pyx3.run$2(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:287)
at org.python.pycode._pyx3.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyBaseCode.call(PyBaseCode.java:308)
at org.python.core.PyFunction.function___call__(PyFunction.java:471)
at org.python.core.PyFunction.__call__(PyFunction.java:466)
at org.python.core.PyFunction.__call__(PyFunction.java:456)
at org.python.pycode._pyx3.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx3.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:259)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Caused by: java.lang.IllegalArgumentException: invalid bin position specified
at net.imglib2.histogram.Real1dBinMapper.min(Real1dBinMapper.java:237)
at net.imglib2.histogram.Real1dBinMapper.center(Real1dBinMapper.java:265)
at net.imglib2.histogram.Real1dBinMapper.getCenterValue(Real1dBinMapper.java:151)
at net.imglib2.histogram.Real1dBinMapper.getCenterValue(Real1dBinMapper.java:49)
at net.imglib2.histogram.Histogram1d.getCenterValue(Histogram1d.java:300)
at net.imagej.ops.threshold.AbstractComputeThresholdHistogram.compute(AbstractComputeThresholdHistogram.java:53)
at net.imagej.ops.threshold.AbstractComputeThresholdHistogram.compute(AbstractComputeThresholdHistogram.java:41)
at net.imagej.ops.threshold.ApplyThresholdMethod$IsoData.getThreshold(ApplyThresholdMethod.java:155)
at net.imagej.ops.threshold.ApplyThresholdMethod$IsoData.getThreshold(ApplyThresholdMethod.java:134)
at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:52)
at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:43)
at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:136)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.python.core.PyReflectedFunction.call(PyReflectedFunction.java:188)
... 31 more

Hi, I try to run the MiNA, But I failed everytime
Could you help me to figure out this problem?
Thank you!

[INFO] Reading available sites from https://imagej.net/
[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Yanqiao Lu store\fiji-win64\Fiji.app\jars\Lib\eztables_init_$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx0.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx0.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Yanqiao Lu store\fiji-win64\Fiji.app\jars\Lib\eztables_init_$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx1.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx1.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Yanqiao Lu store\fiji-win64\Fiji.app\jars\Lib\eztables_init_$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx2.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx2.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Yanqiao Lu store\fiji-win64\Fiji.app\jars\Lib\eztables_init_$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx3.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx3.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): C:\Yanqiao Lu store\fiji-win64\Fiji.app\jars\Lib\eztables_init_$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx4.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx4.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

Mitochondrial footprint output is inaccurate when 3D stacks don't have padding. This bug is being fixed and will be solved in the new release of MiNA.

The thresholding method selection on the settings dialog does not alter the method used in analysis as expected. This issue was found while processing a 2D image and has been reproduced on a 3D stack as well.

Potential Fix:
Separate the method selection from the binarization step. Need to dig up the documentation on this command to see why this is.
From:

run("Make Binary", "method=" + THRESHOLD_METHOD + " background=Dark");

To:

setAutoThreshold(THRESHOLD_METHOD)
run("Make Binary", " background=Dark");

Hello,
I need to run MiNA on many 3D images. However, the 3D viewer starts everytime. Would that be possible to include a tick-box that would prevent the 3D viewer to pop up? That way, I could run MiNA on several images quicker.

That feature would be much appreciated. But, the perfect feature would be to prevent the 3D viewer AND run MiNA on a folder that contains many 3D images.

Thanks in advance for your response, and thank you for your amazing work.
Best regards,

Hello,

When I try to run MiNa from Fiji, I get this error, what could be?

Thanks

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): /Applications/Fiji.app/jars/Lib/eztables/init$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx0.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx0.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

I installed it following the instruction, but I got a exception and can't run it. The exception is as follow:
(Fiji Is Just) ImageJ 2.3.0/1.51w; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 67MB of 12135MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)
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:303)
... 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.NullPointerException
at org.scijava.ui.swing.widget.SwingNumberWidget.lambda$suitableFormat$0(SwingNumberWidget.java:344)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.reduce(ReferencePipeline.java:479)
at java.util.stream.ReferencePipeline.max(ReferencePipeline.java:515)
at org.scijava.ui.swing.widget.SwingNumberWidget.suitableFormat(SwingNumberWidget.java:344)
at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:127)
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

Hello.
I am a Japanese college student and I am conducting research related to mitochondrial morphology in muscle cell(C2C12).

I am very grateful that I have used Mina that you developed very usefully.

I am planning to use Mina in myotube cells in this study, but is MiNA appropriate to use it?
If you do not mind, I would like to ask your opinion

Specifically, I am planning an experimental design to compare mitochondrial morphology of the control group (myotube cells) with drug administration group (muscle atrophic cell) by MiNA.

I would be pleased if you could reply.

I am getting the following error, could you please suggest a work around this?

[ERROR] Traceback (most recent call last):
File "Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py", line 20, in
ImportError: compiled unit contains version 37 code (38 required): /Applications/Fiji.app/jars/Lib/eztables/init$py.class

at org.python.core.Py.ImportError(Py.java:329)
at org.python.core.imp.readCodeData(imp.java:396)
at org.python.core.imp.createFromPyClass(imp.java:284)
at org.python.core.imp.loadFromSource(imp.java:951)
at org.python.core.imp.find_module(imp.java:769)
at org.python.core.imp.import_next(imp.java:1158)
at org.python.core.imp.import_module_level(imp.java:1350)
at org.python.core.imp.importName(imp.java:1528)
at org.python.core.ImportFunction.__call__(__builtin__.java:1285)
at org.python.core.PyObject.__call__(PyObject.java:433)
at org.python.core.__builtin__.__import__(__builtin__.java:1232)
at org.python.core.imp.importOne(imp.java:1547)
at org.python.pycode._pyx2.f$0(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py:291)
at org.python.pycode._pyx2.call_function(Plugins/StuartLab/MiNA_Scripts/MiNA_Analyze_Morphology.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:157)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$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)
at java.lang.Thread.run(Thread.java:748)

Never mind I figured out what I was doing wrong.

Hello.

I'm trying to analyze mitochondrial morphology. I have a capture that capo to binary image, and then in the plugins tab I try to run the MiNA Analyze Morphology. However, the "Exception" window opens with this message:

(Fiji Is Just) ImageJ 2.3.0/1.53q; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 75MB of 6020MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)
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:748)
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:303)
... 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.NullPointerException
at org.scijava.ui.swing.widget.SwingNumberWidget.lambda$suitableFormat$0(SwingNumberWidget.java:344)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.reduce(ReferencePipeline.java:479)
at java.util.stream.ReferencePipeline.max(ReferencePipeline.java:515)
at org.scijava.ui.swing.widget.SwingNumberWidget.suitableFormat(SwingNumberWidget.java:344)
at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:127)
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

On the other hand, in the console I get the following message:

Exception in thread "Run$_AWT-EventQueue-0" java.lang.RuntimeException: Macro canceled
at ij.IJ.abort(IJ.java:2492)
at ij.IJ.testAbort(IJ.java:429)
at ij.IJ.run(IJ.java:328)
at ij.text.TextPanel.doCommand(TextPanel.java:540)
at ij.text.TextPanel.actionPerformed(TextPanel.java:498)
at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
at java.awt.MenuItem.processEvent(MenuItem.java:628)
at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:357)
at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:345)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:763)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

I checked the readme and all the files are where they should be.

Help please and thank you very much in advance.

Greetings.