Heat Map

[puckwijnia]

Hi! I was wondering if it's possible to make a heat map out of the SHARP Track?

[philshams]

Hi -- could you be more specific?

[puckwijnia]

I'm using the SHARP track to do a cell lineage tracing experiment, but the (over)expression in the cerebellum is so high that instead of cell counting I'm thinking of making a heat map to show the expression. I've registered 'my brains' to the allen brain atlas, so now I'm wondering if it's possible to turn this into a heat map? Thanks for your reply!

[philshams]

That definitely sounds doable. For example, you could take your registered, fluorescent image channel (assuming you had this as an additional color channel that got registered alongside the brain-tissue-stain color channel, it will be one channel of the image that is saved in the 'processed\transformations' folder). Then you could apply the MATLAB function imagesc (https://uk.mathworks.com/help/matlab/ref/imagesc.html).