Thank you Beth for looking into my pipeline. I really appreciate it.
I did check the probably map from ilastik and seem fairly accurate. In terms of CP, I would try overlay outlines + save images module as you have suggested. Thanks for your tip!
In brief, I’m trying to establish a co-culture system whereby the xenograft are supported by MSCs. In the past, we observed the monoculture won’t survive the drug treatment thus there was no meaningful results. So in this co-culture system, we are hoping to do have a viability readout in a high throughput imaging manner.
We have been trying to use a dye called CyQUANT which stains the viable cells (https://www.thermofisher.com/au/en/home/brands/molecular-probes/key-molecular-probes-products/cyquant-cell-proliferation-assays.html). The reason why I’m looking at mean Intensity is because CyQUANT tends to have a gradient of signal. It composes of a fluorescent dye which binds to DNA and a suppressor which is permeable to leaky cell membrane, binds to CyQUANT and suppresses it from fluorescencing. The amount of inhibition also depends on how leaky of the membrane is and how much suppressor is present, and the position of the DNA. I spoke to the company technical support and confirmed this and thus the dye is not really as simple as “on or off”. What do you think about this? Have you come across any experiment which uses dye with similar mechanism?
As for adding the dose information in the metadata module, would you be able to explain a bit more? Sorry I’m still quite new to imaging analysis…