CSHL Single Cell Biology Core
Getting Started with COMET data
Check out some tips on how to start analyzing your Lunaphore COMET data
What should I do first?
The raw data that comes off of the Lunaphore Comet will include autofluorescence images, and possibly secondary only scans of the same piece of tissue. The most common first step in analyzing your data is performing a background subtraction using these images. If you're a Windows user, you can perform this process yourself using Horizon viewer. If you are not a Windows user you can request we provide you with the background subtracted versions of your data. You will want to use the background subtracted data for most applications including visualizing the data as well as marker quantification.
Available for Download (Windows only)
Python-Based
Background Subtration
Check out on github
What should I do next?
Now that you have a background subtracted image, the next step is normally segmentation. This is normally nuclei based segmentation. Once the nuclei have been segmented, you can predict the cell boundaries, then quantify the pixel intensity of each marker within those cells.
Paid subscription available through Biotechne
Paid use available through the Histology Core
We can help!
We can help segment your samples or you can do the segmentation yourself on your own HPC with these tools
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Qupath
How do I move into more complex analysis?
Now that you've done some segmentation and quantification you can move to more complex types of analysis like data visualization, as well as clustering, cell type annotation and more complex analyses.
Paid subscription available through Biotechne
Paid use available through the Histology Core