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Color the CCF by segment #6

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jcfr opened this issue Jun 27, 2018 · 3 comments
Closed

Color the CCF by segment #6

jcfr opened this issue Jun 27, 2018 · 3 comments
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Status: No Action When the resolution is to not do anything Type: Feature Request Request for a new feature

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@jcfr
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jcfr commented Jun 27, 2018

After creating the color table (See #3), there are few approaches to generate the "segments" and have them displayed in 3D:

  1. Import the label map into segmentation module and generate corresponding segments
  2. Use model maker to generate the model for each "non air" label listed in the color table

First, I suggest to evaluate approach 1. Depending on the time it takes, we could look into saving the generated segmentations and bundling it with the application. If loading the segmentation file also take times, some profiling would also be needed.

@dyf
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dyf commented Jul 12, 2018

This query downloads all of the structures in the structure ontology this atlas uses:

http://api.brain-map.org/api/v2/data/Structure/query.json?criteria=[graph_id$eq1]&num_rows=2000

Each record looks like this:

{
	"acronym": "eps",
	"atlas_id": 690,
	"color_hex_triplet": "CCCCCC",
	"depth": 2,
	"failed": false,
	"failed_facet": 734881840,
	"graph_id": 1,
	"graph_order": 1218,
	"hemisphere_id": 3,
	"id": 1000,
	"name": "extrapyramidal fiber systems",
	"neuro_name_structure_id": null,
	"neuro_name_structure_id_path": null,
	"ontology_id": 1,
	"parent_structure_id": 1009,
	"safe_name": "extrapyramidal fiber systems",
	"sphinx_id": 1219,
	"st_level": 2,
	"structure_id_path": "/997/1009/1000/",
	"structure_name_facet": 738013408,
	"weight": 8690
}

The one you care about for colors is color_hex_triplet. The id field is what you'll find in the annotation volume.

@dyf
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dyf commented Jul 12, 2018

Ah sorry, I see there is a separate issue for creating the color table -- replicating my comment there.

@jcfr
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jcfr commented Sep 7, 2018

Closing. Duplicated of #10

Following last discussion, we will not generated 3d models and will not enable volume rendering

@jcfr jcfr closed this as completed Sep 7, 2018
@jcfr jcfr added Type: Feature Request Request for a new feature Status: No Action When the resolution is to not do anything labels May 30, 2019
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