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saalfeldlab / n5-ij

ImageJ convenience layer for N5
BSD 2-Clause "Simplified" License
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Issue opining up h5 file using N5 plugin - images are blank #80

Closed Chriswang0904 closed 3 months ago

Chriswang0904 commented 3 months ago

Hi! I'm trying to open some h5 file through import->N5 on image J, but the images turned up to be blank. The file is able to open up properly using the import->HDF5. I wonder what the issue is?

Context: My dataset is very large and exceeds the HDF5 plugin size limit, so I want to use the N5 plugin and use its virtual stack function. The N5 opens the file as blank no matter if the file size is big or small, or if I use virtual stack or not.

Thank you very much!

Screenshot 2024-05-14 at 4 25 38 PM Screenshot 2024-05-14 at 4 25 44 PM Screenshot 2024-05-14 at 4 25 55 PM Screenshot 2024-05-14 at 4 26 22 PM
bogovicj commented 3 months ago

Hi @Chriswang0904 ,

It may be that the brightness / contrast is set strangely and not that the image data is missing. After opening the image, can you please try Image > Adjust > Brightness/Contrast and hit Auto. Please let us know if that helps or if the issue persists.

Chriswang0904 commented 3 months ago

Hi @Chriswang0904 ,

It may be that the brightness / contrast is set strangely and not that the image data is missing. After opening the image, can you please try Image > Adjust > Brightness/Contrast and hit Auto. Please let us know if that helps or if the issue persists.

This worked… thank you!!

bogovicj commented 3 months ago

Thanks for reporting back!

In the future, I'll try to have the plugin pick reasonable brightness / contrast values after opening...