[ome-users] DM4 reader pixel height/depth scale errors

[David Gault (Staff)]

Hi Martin,

Thank you for getting in touch, I’m afraid this is a known issue that we have seen before. We do have a development task scheduled to update the metadata parsing of DM4 files and it is our intention to have this issue resolved in a future Bio-Formats release.

Thank you for uploading the file to QA.16940, this will certainly be useful and help aid development.

With Thanks,
David

On 30 Nov 2015, at 16:59, Martin Jones <Martin.Jones at crick.ac.uk<mailto:Martin.Jones at crick.ac.uk>> wrote:

Hi,

thanks to all for the excellent work! Unfortunately I am still finding a bug in reading DM4 files. The image loads fine in the viewer, but the reported Pixel Height and Voxel Depth dimensions are incorrect. Specifically, the Pixel Height seems to give the value I’d expect for Voxel Depth (0.05um in the example I uploaded to QA.16940) while the Voxel Depth is reported as 5.0um. The Pixel Width is reported correctly and since the x,y dimensions are the same I have enough information to impose the correct width, height and depth so I have a workaround for now. It looks as though the raw metadata only records FOV and number of pixels so I guess there’s a calculation being performed somewhere to get the individual pixel size?

I have Bio-Formats version 5.1.6-DEV installed on an up-to-date Fiji installation.

Many thanks!
Martin




Dr. Martin Jones

Electron Microscopy STP
The Francis Crick Institute
Lincoln's Inn Fields Laboratory
44 Lincoln’s Inn Fields
London WC2A 3LY

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