Bio-Formats doesn't open highest resolution Leica *.scn series

Hi everybody,

I have an issue with the Bio-Format plug-in. I want to use it to open the output file of the Leica slide scanner, which is *.scn. Apparently, this is a “pyramidal tiff”. Please forgive me, if I’m technically incorrect.

Anyway, when importing the scn file, there is a couple of so-called “series” which I can select for import. Besides a couple of overview images that are saved within this file, there is several images of the area that was scanned in detail. These are probably the “pyramid”. I can open these up to the second highest resolution (which is 11264x16192). However, and this is the problem: I can not open the highest resolution image (45056x64768).

Opening the second highest image takes a couple of minutes, between 4 and 5. I would image that a picture with 16 times the amount of pixels would then take significantly longer. I have been waiting for 2hrs. Nothing happens. The activity monitor (btw, I’m on a mac) does not show any activity of Fiji (it does use a lot of computing power when opening the lower resolution image).

I have until tomorrow evening 21:30 to get an image out of this file that can be printed on DIN A4 with 300dpi. If I won’t, there goes the journal title page with my histology staining on it. So any help is very highly appreciated!

Best regards,
Gero

Welcome to the forum, @Gero_Knittel!

The problem is that 45056x64768 is larger than the 2 gigapixel limit of ImageJ 1.x. So you will not be able to open the entire image plane at once.

What you can do is use the “Crop on import” option to open the image in tiles. In your case, four tiles of 22528x32384 should work fine. Even two tiles of 45056x32384 (i.e., the top and bottom halves of the plane) should be under the 2 Gpix limit.

Of course, your journal will need to figure out how to put the tiles back together again…

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Dear Curtis,

a (much too) late “thank you very much!”

This solved the problem (it did so in time, I tried it immediately of course, only my response is delayed). A colleague had even told me about a “2gig file limit”, which I thought meant 2 gigabytes, not 2 gigapixels.

Anyway, I can now have my title page, thanks to your fast and competent help.

Best regards,
Gero

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Awesome, glad things worked out for you! :sunny: