[ome-users] Problems with SCN files

Joseph Jacobs j.jacobs at cs.ucl.ac.uk
Sat Dec 6 15:00:05 GMT 2014

Hey all,

I am having some problems opening Leica SCN files with Bio-Formats. So I have quite a few SCN files that I want to convert to TIFF/BigTIFF files. Each SCN file has 6 series which are basically the same image at different magnifications.

The first problem seems to be with reading the file. A lot of noise is introduced into the image when I read it with showinf. Tried reading the files on the demo server and I get the same results (https://dl.dropboxusercontent.com/u/15317306/noise%20sample.png). Has any one seen this problem before? The noise seems to be most common in background regions and only sometimes occurs on the tissue itself. Perhaps it’s an issue with decompression?

The second problem I have been having is with the actual saving of TIFF/BigTIFF files. When I try to save the 6 different series to TIFF files, the two series with the highest magnifications are saved wrong. Here are samples of high (https://dl.dropboxusercontent.com/u/15317306/high.tiff) and low (https://dl.dropboxusercontent.com/u/15317306/low.tiff) magnification. You can still see the noise on the low magnification but it is largely correct. Whereas with the high magnification image, there seems to be some information on the blue channel and noise on the red channel. Anyone know what I am doing wrong here? The command I am using to convert the images is as follows:

bfconvert -series 3 filename.scn filename.tiff

Any help/pointers would be greatly appreciated.


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