Polygon tool distorts series read into Fiji via the Bio-Formats Importer plugin


I am attempting to use the polygon tool to select a region in an image that was taken on an Aperio slide scanner. The images are saved as SVS files. The Bio-Formats Importer plugin has been used to read these files into Fiji. Application of the polygon tool to the resulting image series causes distortion of the images, as depicted in the attached file.
I have tried restarting Fiji; restarting my computer; and re-installing the Bio-Formats plugin. These steps have failed to correct image distortion.
Has anyone encountered this problem before? What might be a viable solution?

I would be grateful for any insights that you are able to lend!

Thank you,


Hi @Meggin_7, this isn’t something Ive ever seen before. Does it occur consistently every time? Do you know if it happens for other formats?

Hi @dgault,
The Bio-Formats Importer plugin opens four series at the resolutions, 21509.11x6205.19 microns, 10720x8076 pixels, 2680x2019 pixels, and 511,13x385.23 microns, respectively. I do not know why the units vary. The distortion only occurs upon application of the polygon tool to the 21509.11x6205.19 microns series. This malfunction does occur consistently. The polygon tool functions properly in the other image series and in TIFF and JPEG file formats.

Thank you for your response!


If you are able to upload the sample file to https://www.openmicroscopy.org/qa2/qa/upload/ I can test it to see if I can reproduce the issue.