Hi, I’d like to start by thanking you for developing CellProfiler, I still can’t believe such a useful piece of software is available for free. I’d also like to apologise for the length of this post in advance.
So, now my problem:
I am using high content microscopy to image slide samples of whole ex-vivo of embryonic mouse pancreas, each exposed to a different condition. My aim is to analyse the effects of each condition on amylase expression in the developing tissue. There are 2 tissues/conditions per slide and, using a template, I can image 4 slides per imaging run (see my layout image provided).
Unfortunately due to the irregular size, shape and placement of the tissues on each slide, I have to capture composite images of each tissue individually, with each tissue consisting of between 6-20 smaller images each.
Additionally the tissue is extremely dense so I have used a combination of E-cadherin and amylase immunofluorescence staining to identify the cell outlines in each tissue and save each outlined cell as an object. I then determine the intensity of amylase florescence within each object.
The problem comes when I want to process my images using cell profiler. If I process all the images I have collected together at once I end up with a huge database of tens of thousands of different objects with no efficient way of associating each image/object with each tissue. I have tried separating each set of images into batches by having the software recognise each position within my template as a different “well” and processing the images from each “well” separately. However because I have re-used the template for several sets of tissues, often two unrelated tissues will be processed together in the same “batch”.
What I want to know is, is there a way I can identify or label each set of images as belonging to a specific tissue, thus making it easier to pull them out of the database when I have finished processing.
JamesE-cad identifier Amylase.cpproj (299.8 KB)Uploading…