Something is wrong with the SaveImage module


#1

I’m using CP2.2.0 on a PC equipped with windows 10, Ryzen CPU.
At first I’ve got weird results after overlaying objects and save the overlaid image. In order to trace where the problem is, I just read an image and save it per se. so my pipeline contains just one module, SaveImages. But this is what I got!


#2

Please post your pipeline and input image and the resulting saved image file. That is certainly funky!


#3

test.cpproj (89.5 KB)

thanks!


#4

This is what I get when I open your input image in both FIJI (shown) and CellProfiler (not shown)- are you getting this problem across multiple images, or is it possible that just this one image has been corrupted?


#5

all the images! no exception. but when I open this image in windows (painter, XnViewer and Windows default photo viewer) and in Ubuntu default viewer, it looks normal, not like that. i’ve been using CP for a year, and this kind of thing has never happened.

  • I tried changing the input file format to .jpg, and it seems to work normally.

#6

It looks fine in my Windows photo viewer as well, but the fact that it looks the same in CP and in ImageJ makes me think it’s a Bio-Formats (the library both CP and FIJI use for image loading) issue.

When I try to open your image in FIJI by just dragging and dropping, I get the error below. Opening with FIJI’s built in version of Bio-Formats gives the image I posted above. Were these taken in a different way than your previous images, did your microscope perhaps get a software upgrade recently, etc?

The good news is that using CP 3.0 (which is available in Beta on our website) and which has a newer version of Bio-Formats that CellProfiler 2.2 seems to open your image just fine (below), so if you can’t figure out how to get your microscope to export a TIF that’s compatible with older versions of Bio-Formats (or as a PNG or other lossless format- JPGs are lossy, I’d avoid them if possible!) you can use CP 3.0 for your future work.


#7

thank you for your interest. I’ve created the input image files using ‘extract region’ functionality of Aperio ImageScope and yes, there there has been subtle changes when creating the the recent images! originally the extracted tif files contained unnecessary information such as thumbnail and label image. i’ve recently discovered an option not to export the information and applied it in order to reduce the size of images… anyway good to here that CP 3.0 can handle my reduced images :slight_smile:


#8

thank you for your interest. I’ve created the input image files using ‘extract region’ functionality of Aperio ImageScope and yes, there there has been subtle changes when creating the the recent images! originally the extracted tif files contained unnecessary information such as thumbnail and label image. i’ve recently discovered an option not to export the information and applied it in order to reduce the size of images… anyway good to here that CP 3.0 can handle my reduced images :slight_smile:

Nice! Thanks for the update.