Synapses in neuroglancer, pre and post in two colours

From a DVID synapse instance to a link that shows the selected neuron’s output synapses in one colour and its inputs in another. Four commands; the viewing guide explains each choice in depth.

You need a DVID node with a synapse annotation instance and a precomputed segmentation exported from the same node, so body ids agree. The paths below are placeholders.

1. Choose the bodies

DVID cannot cheaply list every body worth fetching, so the list comes from its synapse index:

neu-mark select-bodies --src dvid://dvid.example.org/abc123/synapses \
    --min-synapses 10 --out bodies.csv

2. Fetch their synapses into tables

neu-mark points --src dvid://dvid.example.org/abc123/synapses \
    --bodies bodies.csv --out syn/ --connections

syn/ gets a points table (one row per T-bar or PSD) and, with --connections, a connections table pairing each T-bar with its partners. The tables are the durable record: the next step can be rerun with other settings without refetching.

A partner on a body outside bodies.csv is fetched with its synapse, but its body is unknown. --all in place of --bodies fetches every synapse of the instance and looks up every element’s body, so nothing is missing and every partner is named; pass the body list to step 3 as --listed bodies.csv to keep telling the two apart.

3. Write the annotation source

neu-mark annotation-source --tables syn/ \
    --dst s3://my-bucket/seg/synapses --voxel-size 8,8,8 --verify 100

One line per connection, from the presynaptic site to the postsynaptic one, indexed by body_pre and body_post so a viewer can fetch one body’s synapses directly. --voxel-size is the segmentation’s, so the lines land on it. --verify 100 reads 100 annotations back through the source’s own info: a wrong key would otherwise leave the viewer empty while every file looks correct.

4. Make the link

neu-glance gen --seg s3://my-bucket/seg --annotations s3://my-bucket/seg/synapses \
    --annotation-shader synapse --segments 12345 --format url

One layer shows the selected bodies’ synapses, inputs and outputs together. The synapse shader colours presynaptic sites red-orange and postsynaptic sites blue, with a yellow line between them. Its show_pre / show_post boxes show either end alone (without the line), show_line turns the line off, and the layer’s Annotations tab filters on each relationship separately: body_pre alone gives the selected bodies’ outputs, body_post alone their inputs.

Add --presyn-postsyn for two more layers, presyn and postsyn, each filtered on one relationship and showing only that end. Together they mark the selected bodies’ own output and input sites without the partners’ ends, which is what you usually want in the 3D view.

With annotation-source --roi-spec SPEC.toml (and points fetched with --rois), the source also carries each synapse’s ROI and top-level neuropil, and the shader gains color_by_neuropil and color_by_neuropil_part; color_by_neuron_id and color_by_tbar_fanout need nothing extra. With --listed, it gains hide_unlisted (hide synapses with neither end on a listed body) and hide_unlisted_partner (keep only synapses between listed bodies).

In the viewer

• Nothing shows until a body is selected. The layers follow the segmentation’s selection; --segments selects some up front. To show everything, untick the filter in a layer’s Annotations tab, or pass --no-filter-by-segmentation.

• The colours, marker sizes and a confidence threshold are controls in the layer’s Rendering tab (pre_color, post_color, line_color, pre_size, post_size, min_conf), next to the color_by_* boxes.

• Synapses with no confidence value stay visible at every threshold. They are mostly added by hand, so unknown confidence is not treated as low.

• Some lines have a partner outside bodies.csv. They are kept, since the synapse is real; annotation-source --drop-partial leaves them out.

A link carries its whole state, so it can get long. --format state --out state.json writes the state instead, and neuroglancer opens one stored at a URL given after #! (…/#!s3://my-bucket/seg/state.json) if the object is readable without credentials and its bucket allows CORS.