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Mechanobiology-Lab / BatchDeconvolution

Fiji plugin for increasing deconvolution workflow
GNU General Public License v3.0
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Error using BatchDeconvolution - Null ImagePlus passed to concatenate(...) method #6

Open alentheboredone opened 2 years ago

alentheboredone commented 2 years ago

Hi,

I'm relatively new to Fiji and deconvoluting images with it. I have stumbled your publication and wanted to give this a shot, but I get these errors during the re-combination step of the process (see attachment). Can you perhaps support me in this? Many thanks.

I have also added an exemplary image, inside the zip-file you will find tiff image.

error messages using BatchDeconvolution.pdf center.zip

RaquelParadaPuig commented 2 years ago

Hello,

I had the same problem, and I'm not sure why I can't solve it. The plugin does everything rigth unil is time to concatenate the images.

Any ideas?

sorenhejgaard commented 2 years ago

Hi,

I deleted all folders and started over by downloading the following folder "Souce code (zip)" at https://github.com/Mechanobiology-Lab/BatchDeconvolution/releases/tag/v1.03 [https://opengraph.githubassets.com/fe8f0a053a64771dd1075fb11aed392adc8cf246638478827eb2ddd2ba417aaa/Mechanobiology-Lab/BatchDeconvolution/releases/tag/v1.03]https://github.com/Mechanobiology-Lab/BatchDeconvolution/releases/tag/v1.03 Release BatchDeconvolution v1.03 · Mechanobiology-Lab/BatchDeconvolutionhttps://github.com/Mechanobiology-Lab/BatchDeconvolution/releases/tag/v1.03 Corrected file import for Mac OS and Linux (not tested) Corrected incorrect recognition of slices, frames and channels at combinig stage Extended java virtual machine memory allocation for deconvol... github.com

After doing this, it worked for me.

regards, Søren

Fra: RaquelParadaPuig @.> Sendt: 1. august 2022 13:38 Til: Mechanobiology-Lab/BatchDeconvolution @.> Cc: sorenhejgaard @.>; Comment @.> Emne: Re: [Mechanobiology-Lab/BatchDeconvolution] Error using BatchDeconvolution - Null ImagePlus passed to concatenate(...) method (Issue #6)

Hello,

I had the same problem, and I'm not sure why I can't solve it. The plugin does everything rigth unil is time to concatenate the images.

Any ideas?

— Reply to this email directly, view it on GitHubhttps://github.com/Mechanobiology-Lab/BatchDeconvolution/issues/6#issuecomment-1201086205, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZU7OAPJTQDKKKYDZZTIONTVW6ZLNANCNFSM5WZTLUIQ. You are receiving this because you commented.Message ID: @.***>

RaquelParadaPuig commented 2 years ago

Thank you Søren! I tried this way but it does not work. I'm not sure of what I'm doing wrong. Can I ask if you used the "Source code(zip)" folder instead of following the instalation instructions including the 3 folders containing plugins DeconvolutionLab2, PSF Generator and BatchDeconvolution?

I think I don't really understand what to do with this "Source code (zip)".

I'll keep trying to see if I can get somewhere with this. Thanks!!!

Raquel.

shreygandhi1990 commented 1 year ago

Hi @ZbigniewBaster @RaquelParadaPuig and @sorenhejgaard,

I too get the same error. I tried to install it using the BatchDeconvolution_1.03.zip file but still got this error. I am not proficient with Java and could not compile the source code to produce the .jar file. Please let me know if you were able to solve the issue.

Thanks!! Shrey

sorenhejgaard commented 1 year ago

Hi shrey,

Unfortunately, we didn’t.

Best Søren

Fra: Shrey Gandhi @.> Sendt: Tuesday, March 21, 2023 4:26:04 PM Til: Mechanobiology-Lab/BatchDeconvolution @.> Cc: sorenhejgaard @.>; Mention @.> Emne: Re: [Mechanobiology-Lab/BatchDeconvolution] Error using BatchDeconvolution - Null ImagePlus passed to concatenate(...) method (Issue #6)

Hi @ZbigniewBasterhttps://github.com/ZbigniewBaster @RaquelParadaPuighttps://github.com/RaquelParadaPuig and @sorenhejgaardhttps://github.com/sorenhejgaard,

I too get the same error. I tried to install it using the BatchDeconvolution_1.03.zip file but still got this error. I am not proficient with Java and could not compile the source code to produce the .jar file. Please let me know if you were able to solve the issue.

Thanks!! Shrey

— Reply to this email directly, view it on GitHubhttps://github.com/Mechanobiology-Lab/BatchDeconvolution/issues/6#issuecomment-1478038981, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZU7OAMXEW4MGWPKADLXXDDW5HCAZANCNFSM5WZTLUIQ. You are receiving this because you were mentioned.Message ID: @.***>

ZbigniewBaster commented 1 year ago

Hey Everyone, I was trying recently to figure this out and it seems that there was a problem with one of the Java versions, that the package wasn't fully compatible with. Currently I have installed JDK 18.0.2 and it's mostly working. There is one problem with PSF panel that crashes, when I try to change values. Yet, for now you can export settings file, change values there and load it back and it works. I'm planning to look closer into that and fix it in the near future.

Sorry for keeping you this long without updates. Let me know if getting that Java version helps in your case.

Best, Zbyszek

shreygandhi1990 commented 1 year ago

Hi @ZbigniewBaster, Thank you for your reply.

I installed JDK 18.0.2 and forced Fiji to use it instead of the default java version in the Fiji app folder. However, now I am not able to start Fiji at all. I get the following error when trying to start Fiji:

Warning: falling back to system Java
Unrecognized option: -Xincgc
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

I think it has something to do with the incompatibility between the Fiji app and the java version. Could you maybe also specify the fiji app version on which you tested it.

Best wishes, Shrey

ZbigniewBaster commented 1 year ago

@shreygandhi1990 I just tested it on fresh Fiji, and its the same as the one as I regularly use. Have you tried running deconvolution without disabling Java? When I was writing the software I had a couple of issues, that I ended up addressing windows command line from within Fiji, to run sub-plugins (PSF Geneartor plugin that I use there is the "Matlab" one and it wont run directly from Fiji. The Fiji one didn't have command line input).

Thanks for checking this. I might have another PC that I can test it on. Also my friend recently asked me for the software, so I should hear back from soon how it works.

I'm attaching the version that I used for testing. It should be the same as the latest that I posted here.

Best, Zbyszek BatchDeconvolution.zip

mpd83294 commented 1 year ago

Hi, I am also having this issue. I downloaded the zip file you are using for testing and I am still getting the "Null ImagePlus passed to concatenate(...)" error when it was combining the images.

Not sure what is going on here, any help is appreciated. Thanks!

CocomChan commented 3 months ago

Hello, I tried different Fiji installations, different versions of the Plugin(s) and a an updated JDK. Still getting the same error "Null ImagePlus passed to concatenate(...)"

:(

It is really sad because the plugin looks amazing and it could help me to speed a lot my analysis. If there is any update or possible solution I will appreciate. Thanks