Deconvolving with image ops

Usage & Issues
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#1

Hello,

When I try to deconvolve with the Image Ops plugin, I get the following error message:

[ERROR] Module threw exception
java.lang.NullPointerException
at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:87)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:483)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:242)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:152)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:133)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:138)
at io.scif.convert.FileToDatasetConverter.convert(FileToDatasetConverter.java:66)
at org.scijava.convert.AbstractConvertService.convert(AbstractConvertService.java:125)
at org.scijava.convert.AbstractDelegateConverter.convert(AbstractDelegateConverter.java:53)
at org.scijava.convert.AbstractConvertService.convert(AbstractConvertService.java:125)
at org.scijava.module.DefaultModuleService.load(DefaultModuleService.java:316)
at org.scijava.module.DefaultModuleService.loadInput(DefaultModuleService.java:544)
at org.scijava.module.DefaultModuleService.lambda$loadInputs$1(DefaultModuleService.java:346)
at java.util.ArrayList.forEach(ArrayList.java:1257)
at java.util.Collections$UnmodifiableCollection.forEach(Collections.java:1080)
at org.scijava.module.DefaultModuleService.loadInputs(DefaultModuleService.java:346)
at org.scijava.module.process.LoadInputsPreprocessor.process(LoadInputsPreprocessor.java:58)
at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:154)
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)

Actually, I encountered error messages when I tried to run other filters from Image Ops as well. Has anyone else encountered this error? If so, how did you resolve it? Thank you for your time and attention.

#2

I managed to install image ops, but I’m having difficulty deconvolving. I have tried a wide range of input regularization factors and I have attached the best I could come up with using a regularization factor of -0.01. Has anyone else had problems or success with deconvolving with Image Ops plugins? Also some of the deconvolving options ask for “Input 2”. Is “Input 2” the point spread function? I entreat your advice. Thank you. Here is the link for the data:

#3

Hi @GopherConfocal

Yes, input2 is the point spread function. Do you have a measured point spread funciton you are using?? If so can you share it along with the images? If you are generating a theoretical point spread function do what code or plugin are you using?

#4

Thank you for replying. There’s a python script I found that makes nice PSFs and I put the script, the settings I use, and the PSF image in the Google Drive folder. Thank you so much for your help. I need to deconvolve all three channels. Thanks again!

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