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petersaj / AP_histology

Histology processing
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The step of White-balance slides was not performed #24

Closed Tan-Lao closed 1 year ago

Tan-Lao commented 1 year ago

Hi, Professor Peter.I tried your demo_histology_pipline code, and the slice format is the same as in your video, which is a tiff file and has RGB channels, but when I run it to the AP_process_histology function, I'm just going to extract individual slices, and I'm not going to set the white balance.

Levi PhD Student

petersaj commented 1 year ago

Hi Levi - is the tiff file actually RGB with values 0-255, or does it have separate gray-scale channels for each color? It sounds like it may be RGB, since the pipeline doesn't set white balance on RGB images. I don't remember exactly why I did that - I think it was because RGB images are typically already properly white-balanced since their range is so small. If you're possibly able to send me a sample image, I can have a look at adding in white balance for RGB?

Tan-Lao commented 1 year ago

Hi, Professor Peter. Thank you very much for your reply. I am also aware of this, as you said, the image is RGB, and then the white balance will not be set, I feel like this has no problem for the subsequent processing. I've already fitted the 3D brain. Now there is only one last step: Align histology with electrophysiology. I have some problems, just like other people, I also use SpikeGLX to collect data. So I am currently trying to use alignatlasdata from Enny van Beest.

petersaj commented 1 year ago

It sounds like you don't have any questions for me in that case, I'll close this issue for now but feel free to open it again if something comes up.