Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
Two slices of the same image will report different physical sizes.
Steps to reproduce:
1) Open Fiji
2) Use the baseline Bio-formats Importer (v7.3.0 or otherwise), and open a CZI pyramidal image.
3) Pick any two slices.
4) The physical image dimensions will be different between slices (as the pixel/micron size remains fixed)
@NicoKiaru has a potential fix in in https://github.com/ome/bioformats/pull/4092. For anyone performing measurement/analysis of the smaller image, this requires both knowledge of the issue as well as a posthoc correction.
This issue was first raised on the image.sc forums: https://forum.image.sc/t/incorrect-pixel-scaling-on-czi-image-series/87149
Description
Two slices of the same image will report different physical sizes.
Steps to reproduce:
1) Open Fiji 2) Use the baseline Bio-formats Importer (v7.3.0 or otherwise), and open a CZI pyramidal image. 3) Pick any two slices. 4) The physical image dimensions will be different between slices (as the pixel/micron size remains fixed)
@NicoKiaru has a potential fix in in https://github.com/ome/bioformats/pull/4092. For anyone performing measurement/analysis of the smaller image, this requires both knowledge of the issue as well as a posthoc correction.
Ian.