Image Processing and Quantitation

scope1The other day on the MGI mailing list a question came through about quantitating images. It’s been a few years since I thought about image processing–but one place where I was the bioinformatics specialist I also provided support to cell biologists, and that was a need of theirs.

I hadn’t visited NIH Image recently, and was curious to see what the status was.  Still there.  Still a remarkably unassuming page for something so graphical :) .

I used to run a locally installed copy.  But you can also use ImageJ, a Java version you can run on the web.  The mailing list over there seems pretty active, so that’s nice to see if it is software you might need to use.

The whole thing reminded me of another resource I hadn’t looked at recently but remembered fondly: OME Open Microscopy Environment: http://openmicroscopy.org

As a cell biologist by training I do have a soft spot for these….

If anyone has other suggestions for image processing, let us know.

3 thoughts on “Image Processing and Quantitation

  1. Jennifer

    Hi Max,

    Thanks for pointing out this site. I have not used CellProfiler (http://www.cellprofiler.org/) myself, and Mary is away at a conference until later this week. What I can tell you is that it is from the Broad Institute, which is a great sign. It also seems active, since they had a release as recently as 12/2008. It has a Google rank of 5 (out of ten) which isn’t bad for a somewhat new bioinformatics resource. According to their own description, “CellProfiler cell image analysis software is designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.” It is also freely available, which means the price is nice. If you do decide to try it out, please let us know what you think.

    How about the rest of you – anyone have any experience with CellProfiler that you are willing to share?

    Thanks, and good luck!
    Jennifer

  2. Mary

    Hey Max–

    I have not used CellProfiler: http://www.cellprofiler.org/ Thanks for the tip on that.

    At this meeting I was at I spoke to a couple of people specifically about imaging software. One of the posters was displaying ImageJ results. A drawback that was mentioned was that some of the larger images were tough to manipulate in ImageJ.

    I also learned about some software from Clear Canvas http://www.clearcanvas.ca/ that has image processing capabilities–but I haven’t investigated it enough yet to know about what it can do.

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