Conversion of amnis images to cellprofiler 'lossy'?


After using the protocol set up to convert amnis .cif files to montages easily readable by cellprofiler, I looked at some of the resulting cell images. Using the “View Images” tool in the File menu, it appears that the images have lost resolution during the conversion. Is this the case, or is the image viewer showing lower res images?

Here is a screenshot of what I mean: the images on the left are those viewed in IDEAS, on the right are CellProfiler. Thanks for any advice.


Many thanks for this feedback !

I’ll see what I can improve in the module that handle the images, I’ll let you know soon.



Thanks Minh! I wasn’t sure if I was doing something wrong. Thanks for your help!


Thanks, Darin for pointing this out! It seems the cif reader itself, with which we can pull out images from the cif file, is lossy?! It turns out the same issue (loss of resolution) exists with the matlab-bioformats reader. In Matlab, it’s the bioformats function bfGetPlane.m that actually reads the image, and we simply call it in our Matlab tiling script. We’ll look into it and will do our best to resolve this


Thanks Holger! Good to know where the issue comes from. Thanks for looking into it!


Update for this topic:
After in-depth investigation, we can conclude that there is no resolution loss during stitching.

Users may notice that when opening and zooming the images in IDEAS, the images appear to be higher resolution, but this is because the software has an adjustable DPI setting, which uses interpolation to scale the images up (adding pixels) for display and publication purposes.

This info is updated on Github accordingly.