Image analysis issue


I am encountering a problem where only the minority of images are analyzed after successfully loading the images to the file box. All of the images are jpg files with their dimensions being 1300 by 1030. I have also tried to convert the images into tif files, but again cell profiler will only analyze a small selection (same ones as before).

I would like to figure out why some images are not analyzed and some are when all of the images have been saved the same way.

Attached are two images: cell profile analyzes the 4.jpf file without any difficulties while seemingly ignoring the 5.jpg file.

I would greatly appreciate any advice as to why this would be the case.

Thank you so much,

Neighbouring Cells.cpproj (80.4 KB)

Hi Liz,

According to the project file you posted, NamesAndTypes is set to assign a name (and therefore pass forward for analysis) only to those files which contain “1.JPG” in the filename. So if you have named a bunch of JPGs by numbering them, only those that end with 1.JPG (such as “1.JPG”,“21.JPG”,“33451.JPG”) will be analyzed.

If you want all the numbered JPGs to be analyzed, I suggest changing the file name matching condition to simply “.JPG”.


Also, for your images, I suggest changing some of the settings in IdentifyPrimary, namely:

  • Setting the minimum diameter to 50.
  • Setting “Automatically calculate the size of the smoothing filter” to “Yes”
  • Setting “Automatically calculate minimum allowed distance between local maxima” to “Yes”