Image pre-processing

[veenstje]

Hello, is the lab currently using the MIBI_GUI to assist with image pre-processing (e.g., background removal, denoising, and aggregate removal) or a different method?

[ngreenwald]

We're currently using the AMP package for preprocessing: https://github.com/angelolab/amp.

However, we're working on a new solution that we should have available sometime early in the new year that requires much less manual fine tuning.

[veenstje]

Thanks for the info. It appears this is only supported for macOS. Is there a similar application for windows available? If not, will the newer solution you mentioned be compatible with windows?

[ngreenwald]

IonPath has an option for background subtraction/denoising that works on Windows, but ours does not. The new version will only require a jupyter notebook environment and will work across platforms.

[veenstje]

Ok, I will be eagerly waiting for the new version! Thanks for your help

[ngreenwald]

The new preprocessing pipeline is now live at www.github.com/angelolab/toffy