Slide J problems

Usage & Issues
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#1

Hi all,

I have big .scn images (5-10GB) that I want to analyse with Fiji. I read that it was possible by using SlideJ, but it is not, for me at least.

Do you think is it possible (considering the size of the files?)

What do I have to do? First problem that I had is that the package “SlideJ” has 8 different macros. I also read something regarding “bio-formats”, but since I am absolutely rookie in this kind of programs, I didn’t understand anything,

Which macro do I have to use? What do I have to do after it? Has anyone been able to open .scn images with SlideJ?

Thank you very much.

#2

Hi @andymasde, I am not an expert in SlideJ or its macros. If you want to open images of that size with Bio-Formats directly (via Plugins -> Bio-Formats -> Bio-Formats Importer) then I would recommend selecting “Use Virtual Stack” from the list of memory management options in the importer options window.

#3

Hi. Thanks for your answer. I’ve tried what you recommend. I can’t select “Use Virtual Stack”…it is blocked. I tried to do it without using virtual stack and I am struggling. It says “creating image” but no image is created…at least for now. I have been waiting for 10mins and nothing makes me thing that after it the program will be able to open the image…but we will see…never say never…
Do you have any other idea?

Thanks!

#4

Virtual stack will only help if you have a large z-stack… I’m guessing you have a large 2D whole slide image, in which case you may prefer to give QuPath a try… help is also on this forum with the qupath tag.

1 Like
#5

Hi pete,

Thanks for the answer.

I tried QuPath and it is quite useful for me, I would say. I mean, I can extract regions (larger ones than with other programs) and then I can work with them using Fiji, but for each slide I need to do several extractions.

It is not the ideal solution, but at least is a solution.

Thanks.