Black edge / small area of slice for deepslice

BIOP / ijp-imagetoatlas

ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)

https://abba-documentation.readthedocs.io/en/latest/

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Black edge / small area of slice for deepslice #165

Open NicoKiaru opened 1 year ago

NicoKiaru commented 1 year ago

With RGB images, the black background is not really well adapted for sending to DeepSlice, but also to export registered images:

A white background could be an option.

Also, when the slice spans an area too small, it's not going to give good results with DeepSlice. Running DeepSlice two times could be a solution. Having a way to automatically detect the slice area and put a warning is also an idea, but making a simple autodetection could be hard...

Thanks @PolarBean for noticing!

NicoKiaru commented 8 months ago

Note that one can restrict the region of export by defining a ROI. This works well to run DeepSlice on a rat dataset for instance.