I know that I’ve posted quite frequently in the past few months and and wanted to relay the actual project I’ve been working on (or the main project of several). In the Gregory Rogers lab here at the University of Arizona, condensin is being studied for its role in, you guessed it, condensation of DNA in D. Melanogaster cells. Through manipulation of the various sub-units of the protein as well as blocking of a protein-degrading complex a phenotype has been observed where the DNA turns into these hyper-condensed “gumballs”. I’ve been using the texture analysis of CP to quantify this phenotype and show it to be significantly different than the controls. What I’m wondering may be obvious: has this been done before?
Also, I’ve been tasked with writing a methods section on how the image analysis was done. I’m not sure how much detail to include. In the few papers I’ve skimmed that cited CP all I’ve seen is a few sentences mentioning something like “Image analysis was done using Cell Profiler 2.0” and nothing about pipelines, haralick features or CP Analyst. I want to include a more extensive methods section because CP and CP Analyst have been such great tool for the project. Are there any papers you’ve seen (or written) that have more extensive methods sections? A bit of a novice question: would helping us with the methods section be counted as collaboration or is a citation sufficient?
Lastly, thanks for such a great tool. I’ll be entering the genetics program here at University of Arizona and already know I want to do something in image analysis / computational biology. Your software (and help on these forums) have definitely influenced my research goals.