Https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/

Hello all

I have been trying to do registration according to the instructions on Whole Slide Image (WSI) Registration with ImageJ/Fiji and QuPath. I have installed all the necessary plugins such as bidataviewer-playground, elastix. Installation of Visual C++ redistributable has been problematic.

When trying to open the QuPath project on Fiji, Console opens with an error, which is as follows:

file:/C:/Users/kumaravma/Desktop/Neuer%20Ordner/project.qpproj
sourceFile:C:\Users\kumaravma\Desktop\MEM67_HE22.ome.tif[bf:0 - qp:0]
sourceFile:C:\Users\kumaravma\Desktop\MEM67_PBH1.ome.tif[bf:0 - qp:1]
Attempts to set opener settings for file format OME-TIFF; data location = C:\Users\kumaravma\Desktop\MEM67_HE22.ome.tif
Attempts to set opener settings for file format OME-TIFF; data location = C:\Users\kumaravma\Desktop\MEM67_PBH1.ome.tif
[ERROR] Module threw error
java.lang.NoClassDefFoundError: spimdata/util/Displaysettings
at ch.epfl.biop.bdv.command.importer.QuPathProjectToBDVDatasetCommand.run(QuPathProjectToBDVDatasetCommand.java:145)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
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)
Caused by: java.lang.ClassNotFoundException: spimdata.util.Displaysettings
at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
… 10 more

due to this error, I am unable to continue with the next steps. The BDV sources window does not pop-up either.

It would be great if someone could help!

https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/

Hello @Manu_Kumar,

I can try to help! This missing class (spimdata/util/Displaysettings) is weird. Do you have any other update site installed apart from Bigdataviewer-Playground ? Which ones ?

Can you check in your Fiji.app/jars folder whether you can find the file bigdataviewer-spimdata-extras-0.1.0.jar ?

PS : For formatting your message, you can put the error stack trace in between triple quotes

```
Your stack trace
```

2 Likes

Hi @NicoKiaru

Thank you for your reply!

I had installed BioVoxxel apart from the Bigdataviewer-Playground. I resolved the Fiji issue and completed the transformation. However, now I have been trying to transform the image back on QuPath and I am unable to import ch.epfl.biop.qupath.transform.TransformHelper due to which, the process is incomplete.
I did download the Extensions directory as found on the *\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath* website.
This is the code that was applied on QuPath:

// Get the current image data
def imageData = getCurrentImageData()

// Transfer all matching annotations and detections, keeps hierarchy, 
// transfer measurements (first true parameter)
// allow to use inverse transforms (second true parameter)
TransformHelper.transferMatchingAnnotationsToImage(imageData, true, true)

// Computes all intensities measurements in the new image
def server = getCurrentServer()
TransformHelper.addIntensityMeasurements(getAnnotationObjects(), server, 1, true)

//If the image is RGB, this line can be added to import the correct measurements (DAB, etc.) :
//
//server = new qupath.lib.images.servers.TransformedServerBuilder(getCurrentServer())
//      .deconvolveStains(getCurrentImageData().getColorDeconvolutionStains(), 1, 2)
//      .build()
//cf https://forum.image.sc/t/transferring-segmentation-predictions-from-custom-masks-to-qupath/43408/15

this is the error

1 Like

Ah, at least we are progressing :wink:

Didn’t you forget the first line of the script ?

import ch.epfl.biop.qupath.transform.TransformHelper
2 Likes

Let me know how it goes @Manu_Kumar because the first line missing could be the reason for the error message you observe.

Best,

Nicolas

1 Like

hi, it worked fantastic :sweat_smile: thanks for your help :slight_smile:

1 Like