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reconstrue / brightfield

Reconstruction of biocytin-stained neurons detected in brightfield microscopy image stacks
http://reconstrue.com
Apache License 2.0
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View AIBS brightfield stacks in Neuroglancer #225

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

Cuboid Transformer is sufficient to directly view the Allen's brightfield stacks in Neuroglancer.

Sure Xformer's original goal was to get the brightfield stacks into bossDB but this is even simpler. Just drop Xformer's precomputed cuboids in S3 or GCS or Wasabi and point Neuroglancer at them.

See also #67

oradomskyi commented 4 years ago

Hi John, I have a pipeline for tiff to precomputed to view local tiff stack in Neuroglancer, as well as generate mesh from tiff segmentation labels.

JohnTigue commented 4 years ago

Hi Fraya, Excellent! Is the code available on the web?

oradomskyi commented 4 years ago

Hi Fraya, Excellent! Is the code available on the web?

I would update manual and keep all related files here:

https://gitlab.com/orado/em_segmentation_flood_filling/-/tree/master

JohnTigue commented 4 years ago

Nice work. Thanks. I just did a quick read of manual_neuroglancer. I'll give it a shot soon and report back.