search

BICCN / cell-locator

manually align specimens to annotated 3D spaces
https://cell-locator.readthedocs.io
Other
19 stars 7 forks source link

Adding distinguishing features to atlas regions (lines or color randomization) #117

Open joshusama opened 4 years ago

joshusama commented 4 years ago

What's the problem this feature will solve? For the Allen Mouse Brain Atlas, colors between many regions are indistinguishable.

Describe the solution you'd like Add outlines to atlas regions OR Add a "randomize color" feature to enable contrast

It's impossible for one to draw polygons right on anatomical borders when the atlas color palette doesn't differentiate.

Alternative Solutions The only approaches are

  1. to try and change the contrast (doesn't help here)
  2. use the mouse-over to indicate where a region is (by name) and hope one can remember the location OR just draw it and adjust while trying to use the region-indicating mouse-over function (very time consuming)

HIGH PRIORITY

jcfr commented 4 years ago

Add outlines to atlas regions

Would this be more helpful:

image

jcfr commented 4 years ago

An other approach would be to convert each label into its own object (aka "a segment"):

image

We could also organize these into a tree with the possibility to show/hide any of the segment or a segment and its "child"

These would require us to finalize https://github.com/BICCN/cell-locator/issues/96

joshusama commented 4 years ago

These lines look great.  Ensuring contrast is key, such as in the hippocampus where it kind of gets lost.  Maybe a slider for the line intensity?  Or just go white?  Having the ontology colors does help, and even better if you could activate only specific components from an ontological tree.  Others may have a different opinion based on feedback from our own 3D atlas programs

On Thursday, June 11, 2020, 9:15:11 AM PDT, Jean-Christophe Fillion-Robin <notifications@github.com> wrote:

An other approach would be to convert each label into its own object (aka "a segment"):

We could also organize these into a tree with the possibility to show/hide any of the segment or a segment and its "child"

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.