Cell profiler load has access to different version of image?

Perhaps you know if it’s a camera setting, camera software setting, or something with Cell Profiler.

I took some images, trying to increase the red with the camera software before taking the picture.
I am trying to separate blue from red with a camera, and not with separate filters (using a DAPI/TRITC filter).

The image looks ok when opened with Preview or GIMP, but when the input folder is selected and I open the image using the lower left menu in Cell Profiler, it looks like it probably would if I had never made the change with the camera software.

I’ve uploaded one of the offending pictures, and the cell profiler screen shot.
Any thoughts on what caused this and/or how to fix it?


The reason for this is that images in the CellProfiler window are normalized for display by default. You can see this setting if you right-click on the image, and select “Image contrast” from the pop-up that appears. If you then select “Raw” instead of “Normalized”, the image looks as you would expect. The normalized setting stretches the min and max value of each color channel to 0 and 1, respectively. In your case, it looks like the green and blue channels got excessive stretched with respect to the red. One other thing: This setting only affects the display, and not the actual data values used in the pipeline.

We have selected the normalized view as the default because in many cases, the features of interest are fairly dim. However, we have already made note to have this as a user-selectable preference (or perhaps make the color images show up as Raw by default)