[ome-users] Error: Plane index: 1 must be <1

Sabine Fischer Sabine.Fischer at physikalischebiologie.de
Thu May 8 10:32:02 BST 2014

Dear Bioformats team,

I have a problem with the Bioformats command line tool.

I want to extract individual z planes from Zeiss .czi files and according to the documentation the Bioformats command line tool bfconvert can be used for this. However, I can't get this feature to work. I can convert a whole file from .czi to .tif but I cannot extract individual planes apart from the first one. I use the following code:
bfconvert -z 1 "...\ZStack.czi" "...\converted.tiff"
and as an error message I get
"Plane index: 1 must be <1"
(with -z 0 it works)

[cid:image001.png at 01CF6AAE.C4660DB0]

Also if I try to use the patterns to save all z planes as individual files with the following code:

bfconvert -z 1 ...\ZStack.czi ...\converted%z.tiff

a file with the name convertedz.tiff is saved which contains all z planes.

If I look at the metadata the zSize is recognised correctly and also if  I use showinf.bat or the ImageJ plugin the file is read and displayed correctly. [cid:image002.png at 01CF6AAF.98FE7DF0]

[cid:image003.png at 01CF6AAF.98FE7DF0]

With the ImageJ plugin I can then also export the z planes as individual files.

Ultimately, I want to do this conversion for large czi files (extracting time points, series and z planes) as part of a pipeline so I would prefer to use the command line tool not the ImageJ plugin.

I am using Version 5.0.1 of Bioformats (VCS revision: b5a33f3, Build date: 3 April 2014),
Java version 1.7.0_55 (Java (TM) SE Runtime Environment (Build 1.7.0._55-b13), Java Hotspot (TM) 64-Bit Server VM (Build 24.55-b03, mixed mode))
Windows 7 Professional Service Pack 1 (64-bit)

I have attached a small .tif file for which I get the same problem, but am happy to provide the original .czi file if you let me know how.

If you need any further information, please let me know.

Thank you and best wishes

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