March 2017

Help! Why do my output images seem all black?

Beth Cimini

Double clicking on the output images produced by CellProfiler sometimes opens up a screen in your operating system’s default image viewer that looks all black. This can make it seem like your pipeline didn’t work or didn’t produce the right output. However, this can happen for a couple of reasons:

(a) If you’re exporting objects and have only a few objects in your image
(b) If you’re exporting 16-bit images

This has to do with the fact that most non-scientific photo software is designed to show 256 levels...

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