Example

Example

Editglancer is a small Python package for generating neuroglancer links which depict the edits to a neuron in a PyChunkedGraph. This notebook demonstrates how to use it.

Start a CAVEclient for your datastack, here "minnie65_phase3_v1". Note that you may need to change the datastack to one you have access too. For more information, first visit the CAVEclient tutorials.

from caveclient import CAVEclient

client = CAVEclient(
    "minnie65_phase3_v1",
    pool_maxsize=20,
    pool_block=True,
)

Select a root ID (a neuron in this case) to visualize.

root_id = 864691136487559186

Generate a neuroglancer link to visualize the neuron and its edits.

from editglancer import generate_link_for_root

generate_link_for_root(root_id, client)

Neuroglancer Link

If everything worked the link should take you to a page that looks like this, with merges shown in blue and splits shown in red.

If you right click on the "merge" or "split" layer in the neuroglancer window, you can select individual edits. For splits, the segments which were separated from the root will be shown.

Advanced

If you are familiar with NGLUI, you can also extract the edits and pass them to a statebuilder yourself. For more on NGLUI, see the GitHub page.

from editglancer import get_detailed_operations

operations = get_detailed_operations(root_id, client)
operations.head()

	root_id	op_id	user	timestamp	type	location	n_points	roots	disjoint_roots
0	864691136487559186	94559	161	2020-08-03 14:43:34.305000+00:00	merge	[178936.0, 259568.0, 23569.5]	2	[864691135494087312]	[]
1	864691136487559186	226309	56	2021-04-14 01:32:20.568000+00:00	split	[159415.0, 261368.0, 22931.75]	4	[864691136011127459]	[]
2	864691136487559186	226338	56	2021-04-14 01:41:14.665000+00:00	split	[150491.5, 259895.0, 22283.0]	4	[864691136296957211]	[]
3	864691136487559186	226344	56	2021-04-14 01:46:18.347000+00:00	split	[156857.5, 261701.0, 22775.5]	4	[864691135571396645, 864691135660624624]	[864691135571396645]
4	864691136487559186	279988	56	2021-10-06 22:20:10.203000+00:00	merge	[170666.0, 200516.0, 20531.5]	2	[864691136118737944]	[]

from editglancer import generate_statebuilder

statebuilder = generate_statebuilder(client)
statebuilder

<nglui.statebuilder.statebuilder.StateBuilder at 0x17b723fd0>

statebuilder.render_state(operations, return_as="html")

Neuroglancer Link