Fiji Bioformat Importer does not automatically adjust Physical size for different resolutions

bio-formats
fiji
bug
Tags: #<Tag:0x00007fd5405aaf10> #<Tag:0x00007fd5405aad58> #<Tag:0x00007fd5405aab00>

#1

Hello I am reporting a bug I found in the Bioformat Importer function. When the selected file is opened (regardless of type TIFF, JPEG, ect.) and a resolution that is selected other than the original, the scale of each physical size is not adjusted. For example, as shown below, the original resolution has each pixel in a 15504 by 14263 as .252 microns. However, when converted to a 834x768 resolution the physical size does not adjust accordingly, it remains .252 microns. I fixed this by setting the scale of each pixel to adjust for the change in resolution, in this case I had each pixel equal to (.252*(14263/768))=4.68. This adjustment then resulted in outputs at the given resolution to accurately match the test images I put in.


#3

Welcome to the forum, @sbaygani!

How are you resizing the image? Using Image :arrow_forward: Adjust :arrow_forward: Size…?

I tested by opening the Bridge sample, setting unit of length to feet, setting the value to pixel width/height/depth to 0.1, then running Image :arrow_forward: Adjust :arrow_forward: Size…. Afterward, the physical pixel size (as shown in the Image :arrow_forward: Properties…) dialog adjusted accordingly, to 0.2 width and height, such that the image status still said 51.2 feet x 51.2 feet.


#4

This Bug is a problem for me too.

It occurs for the following image: (The file contains a pyramid / multiple resolutions of the same image)

It’s possible to open different downscaled versions of the image with ImageJ & Bioformats.
But ImageJ pretends the physical pixel size is always the same, independent of th scaling of the image.


#5

The bug is propably inside Bioformats.
The wrong physical pixel sizes can be found in the OME Metadata, provided directly by the Bioformats API.


#6

@dgault @s.besson @bramalingam @melissa What do you think?


#7

This does indeed appear to be a bug within Bio-Formats. We have an existing Trello card (https://trello.com/c/INs2Dw2I/147-incorrect-physical-pixel-sizes-with-pyramids) which raised a similar issue. I will update that existing card as the reports listed here suggest that the issue is independent of format type.