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Neural-Systems-at-UIO / QuickNII

https://quicknii.readthedocs.io
MIT License
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QuickNII: atlasmaps with outlines #21

Closed sharoncy closed 9 months ago

sharoncy commented 4 years ago

I sent an email with more info about this request. Is there a way to export atlas maps showing region outlines?

Tevemadar commented 4 years ago

Assuming you need it for a finite number of images at the moment, I suggest generating the images using some image editor. Steps with ImageJ:

  1. open colorful segmentation image xy_seg.png
  2. Process/Find Edges
  3. Image/Type > 8-bit
  4. Image/Adjust > Threshold..., and pull the upper slider to the far left, Apply. If you untick Dark background, it will also invert the result (to black contour on white background). Auto Local Threshold... (also in Image/Adjust) may achieve a similar result in a couple clicks less
Majpuc commented 4 years ago

Feature will be implemented to a later timepoint

Majpuc commented 1 year ago

Hi, This was requested now from the Fyhn lab at UiO. We could maybe provide a script to do this as many users wish to use this to publish images with delineations overlay in their publications.

Majpuc commented 9 months ago

Could be implemented in VisuAlign, webAlign and WebWarp