[ome-users] Issue when reading czi lines scans

Ponti Aaron aaron.ponti at bsse.ethz.ch
Fri Mar 18 16:25:04 GMT 2016


I attach two small line-scan z stacks Image1.czi and Image2.czi with following characteristics:

Image1 (read properly):
Two channels (green and red)
Actual Dimensions: x y z =512 1 80
Pixel size: x z= 0.208um 0.5um

Image2 (read incorrectly):
One channels (only red)
Actual Dimensions: x,y,z =512, 1, 240
Pixel size: x,z= 0.208um, 0.5um

Image1 can be read properly by bio-formats 5.1.8 (resulting in a 512 x 1 x 80 dataset). Image2.czi is read incorrectly, resulting in a 512 x 1 x 1 dataset instead of 512 x 1 x 240 (the z information is lost). The only obvious difference between the two files is the number of channels.

Thanks for looking into this.

Dr. Aaron Ponti
Software and Data Management Engineer
Image Analysis Specialist
Single Cell Unit
Department of Biosystems Science and Engineering (D-BSSE)
ETH Zürich
Office 2.24
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch
+41 61 387 33 74
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