Avocado Protection (🥑)

[william-silversmith]

Avocado (n.) 1. a delicious buttery fruit 2. a neuron cell body with its nucleus punched out.

Alyssa and I developed an anti-avocado attack plan last night. Here are some of the features:

Given you know there's a soma and you want to know if you are dealing with an avocado, you can march along a number of rays projected from the soma center. If the first different voxel encountered by each ray matches the other rays, you're in an avocado. If they are all different, you're in a non-avocado cell.

Some of the avocado fruits have holes in them, so a simple flood fill is insufficient. Therefore you need to do something more like:

labels = binary_fill_holes(labels)
while not labels[center]:
     labels = morophological_close(labels)
     labels = binary_fill_holes(labels)

For dealing with soma contacting the edge of the volume, once you know you're dealing with an avocado, paint a 1 voxel thick border on the faces touching the edge of the image. Then run binary fill holes.

[william-silversmith]

[shangmu]

Oh man. The poor avocado had its nucleus punched out and you guys are still conspiring to attack it? >_<

[william-silversmith]

We fight dirty.

…

On Thu, Feb 20, 2020, 2:30 PM shangmu ***@***.***> wrote: Oh man. The poor avocado had its nucleus punched out and you guys are still conspiring to attack it? >_< — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#40?email_source=notifications&email_token=AATGQSI3KPUGPLYYLZK6WK3RD3K5LA5CNFSM4KYUAYX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMPYEXY#issuecomment-589267551>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AATGQSIS2K7KMSMT257N74LRD3K5LANCNFSM4KYUAYXQ> .

[william-silversmith]

A 3D view.

[william-silversmith]

Fixing the hole in the avocado fruit is probably unnecessary. We can just do binary_image = fruit + pit

[william-silversmith]

Added in #43