Images/bit-depth scaling




I started using CellProfiler for half a year now and I have to say it is a very good software with many useful tools. A big thank you to the CP team!

I have been using CP in conjunction with ilastik for segmentation of xenografts in a co-culture setting. Our ultimate goal is to establish high content imaging assay for patient screen. There is something which I have been trying to understand but still struggling…Im wondering if anyone can shed some light or share some of your insights into the image/bit depth scaling in CP [0,1] (i.e how CP does this scaling? )

The reason why I am asking is because originally I have been using Harmony in Operetta and according to the specialist, the images from Operetta/Harmony are 16 bit tiffs with 2 bits of 0 (14bit camera). I want to compare the different output (i.e Mean intensity per well) generated from both CP & Harmony but found the numbers are very different (due to diff scaling I suppose). I believe a direct comparison of results in this case may not be suitable but most likely the trend should remain the same? I do not have much imaging analysis background so I am hoping to learn more if possible ( I did ask similar question before but still confused)

Thank you in advance!


Hi all,

I am just using again my (monthly) chance to insist again that it would be really really good if Cellprofiler did not rescale the gray values!