16bit images readin without normalization?

Dear all,

I have a couple of questions in running cellprofiler 2.0.

  1. what is the maximum image size that is allowed in CP2? I compiled a pipeline to process a large bright field image tile, ~20MB, and I got an error message: “error while processing IdentifyPrimaryObjects”. After playing with the pipelines, I figured that if I resize it to ~4MB, it went through all the pipelines without a problem. My computer has Intel Quard Core processor, 8G RAM, currently running Win 7 64bit. I also wonder if it has something to do with my computer hardware or if it is the CP2.0 itself.

  2. When I perform image based feature extraction, I notice that all images, either 8bit or 16bit images, are automatically converted to 0.0000-1.0000 when first read in. This is fine if it is 8bit image (0-255). However, when it comes to 16bit image (0-65535), I’m loosing some precision there, 1/65535= 1.53x10^(-5). I wonder if there is a way to keep the raw image settings when first read in CP2 and let user decide if he wants to convert the image to 0.0000-1.0000 range.



Er Liu, Ph.D
Postdoc Scientist
La Jolla Bioengineering Institute
3535 General Atomics Court, Suite 210
San Diego, CA 92121
Ph: (858) 456-7500 x124
Fx: (858) 456-7540
Email: eliu@ljbi.org

Posts: 1
Joined: Thu Oct 20, 2011 9:03 am

I’ve answered this question over in this thread.