Creating Z stacks out of .vsv files - super noob here, please advise!

Image Analysis
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#1

Dear All!

I recently found out about this forum and I am very happy!

I have 60 .svs files, all in the same plane, all are levels.
I could like to stack them such that I can scroll through them like a CT scan.

Is there a software I can use for this please?
(I am also using the search function here and browsing the thread but was hoping someone can give me a super basic beginner noob a clear answer, a lot of the information you guys and gals have here is very complex for me being so new to this lol)

I was thinking of reaching out to our radiology friends to ask how they stack their CT images and using that concept/IT workflow!

Any guidance is appreciated please!!

#2

What are the sizes of your Z-stacks? I hear BigDataViewer frequently being tossed around for imaging large data sets, but I am not sure if it will handle your specific use case.

Alternatively, Napari might be an option, but it might also take a bit of Python setup as I don’t think it handles SVS by default (although development is rapid and I might have missed something).

Not sure what you mean by this as generally if you have levels and want to make a Z stack, that means different planes. If they are different markers, maybe you want more of a multiplex/channel image?

#3

Hey thanks for the reply.

I have about 60 H & E levels/planes (each level is 5 um) and I want to stack them into a Z stack and scroll through them.

What software is the best for this?
Each image file is like 3-4 gigs lol so kinda big.

#4

I have never used it, but that sounds like something BigDataViewer might be able to handle in terms of size (terabytes), but I don’t know about using svs files.

However, if you cannot open your svs files in FIJI (due to size), that might not be an option until they are converted to another format, as indicated on the linked site.

#5

Awesome!
This is exactly the kind of help I was looking for. I appreciate you taking the time to answer my Q. Have a nice day!!