I’m trying to set up a live cell imaging pipeline using the TrackObjects module in CellProfiler. I was hoping to request help with the following questions:
- Is there a way I can test an analysis pipeline (and the effect of changing specific parameters) with a smaller image set? i.e. visualize the tracks and somehow cross-reference with the imaging videos that I have to make sure that the pipeline is working well? If so, how would I do this?
- Does the community have any suggestions in terms of how I can get this tracking to work well?
I’ve briefly described the system below. Please let me know if I am missing any other critical information needed to provide insight.
I’ve attached representative images of one timepoint of the three channels that I acquired below. A larger temporal sequence can be found in this folder: https://drive.google.com/drive/folders/1SLjWGounzTbyAQTR4Y06c0VNh0swSrs4?usp=sharing . The folder also has the cpproj file that I have developed, a snapshot of it is copied below.
When I run this pipeline through the entire dataset, the results don’t make much sense and I’d like to test it with a smaller dataset and verify if the tracks being generated are reliable.
The images are of three channels. The first one stains the nuclei. The second and third channels can highlight cytoplasmic areas of the cells being imaged. The goal of the pipeline is to get intensity values associated with each cell over the course of the entire movie. As such, I’d like to be confident that the tracking software is working well.
The challenge as indicated before is that when I use this pipeline for the entire dataset, the results are a little dubious. But I don’t know how to verify that the pipeline is working well. i.e. be able to cross reference the tracks with the videos (for instance). Other strategies of cross referencing would be very welcome!
I am sincerely grateful for any suggestions/helpful guidance that the community may be able to provide.
Many thanks in advance!