Generating Expression Masks De Novo

Hello @tylermo @wayne

I’ve been using expression images for large-scale, high-content analysis of cell morphology in the mouse ISH database. I would like to know if there’s a way for me to process my own image data to produce expression-style images.

I’m looking for the code, software, or detailed protocol used to generate these expression images. So far, I have only seen as much detail as the mouse white paper “Informatics Data Processing” and the paper by Ng et al.,(2007).

I haven’t been able to find any code resources in the allensdk. If there’s a Jupyter notebook, or any other resource that outlines the image processing steps such that I could implement that process on my own image data, could you point me to it?

Thanks and best,
MP