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get_config
This function gets the in-house tracertools-format config dictionary for a given datastack. These configs are similar to the metadata available from a datastack's publisher with the get_cave_stack_info function, but created specifically for this package with standardized structure and terminology designed for proofreading-related tasks. Used by many of the other functions in this package. Not all CAVE-hosted datastacks are currently supported. For a list of currently-supported datastacks, use the get_supported_configs function.
Arguments:
-
datastack(string, mandatory)- the name of the CAVE datastack you want the config for
- this name is identical to the one used by the datastack's publisher
Returns:
-
config(dictionary)- the config dictionary for the requested datastack
Each config dictionary will have the following keys:
The official CAVE id number for the datastack's alignment as an integer, if one exists.
The public-facing name of the datastack's alignment used for written materials. Often similar to alignment_name but with capitalization included.
The official description of the datastack's alignment as given by its publisher, if one exists.
The back-end name of the datastack's alignment used in programmatic lookups and analysis. Usually all lowercase.
The formatting structure of the cell info table if one exists. For a list of datastack table format names, you can use the get_supported_table_formats function.
The name of the information table for known cells in a datastack, if one exists.
The name of the dataset used by the datastack.
The official description of the datastack as given by its publisher, if one exists.
The address where the alignment images used for the 2D image layer in neuroglancer are hosted. This address can be pasted into the source field of a neuroglancer image layer to view the corresponding image stack, provided the user has any necessary access to the chosen hosting source. Usually these are electron microscope images. For this reason, some sources will list this as the "em_source".
The address of the local server for the backend data of this datastack. Will often be used in the construction of segmentation and skeleton host urls.
The address where the volume containing any neuropil meshes are hosted, if one exists. These are usually formatted as precomputed static meshes.
The formatting structure of the proofreading info table if one exists. For a list of datastack table format names, you can use the get_supported_table_formats function. Used by functions that pull proofreading data automatically like check_seg_proofread_status.
The name of the table containing a list of all neurons and their current proofreading status, if one exists. Used by functions that pull proofreading data automatically like check_seg_proofread_status.
The address where the (usually) chunkedgraph-linked segmentation is hosted. This address can be pasted into the source field of a neuroglancer segmentation layer to load the corresponding segmentation in both 2D and 3D, provided the user has any necessary access permission.
The address for the link-shortening state service to compress the default full neuroglancer url into shortlinks pointing to saved states, if one exists for this datastack. Shortlinks are more usable with common messaging services which impose character limits, particularly for states with large numbers of annotation points.
The address where the precomputed cache of segment skeletons for this datastack is hosted, if one exists.
The formatting structure of the soma/nucleus info table if one exists. For a list of datastack table format names, you can use the get_supported_table_formats function.
The name of the table with data relating to programmatically-detected somas/nuclei, if one exists.
The address for the official tracer-created legacy-format neuroglancer volume containing single-resolution unsharded static meshes for all the known patches of rough data in a given datastack. Such areas are referred to as "swamps" because they're muddy and difficult to navigate. Useful for triaging lists of segments during proofreading with the calc_seg_mesh_intersect function. Used by the triage_segs function for this purpose. These maps are living documents that may be updated at any time during the life of a datastack as new swamps are found or meshing techniques are improved. As of 2026/10/12 only the brain_and_nerve_cord datastack has a swamp map.
A list of the segment IDs for each of the swamp meshes for the chosen datastack. Useful for turning on swamp meshes during automatic link generation and specifying during analyses like those done during the triage_segs function.
The formatting structure of the synapse info table if one exists. For a list of datastack table format names, you can use the get_supported_table_formats function. Used by functions that pull synapse data automatically, like count_synapses.
The name of the official synapse table for this datastack, if one exists. Can be used with get_cave_table and get_cave_table_info functions. Used by functions that pull synapse data automatically, like count_synapses.
Any notes about the datastack added by the publishers of the tracertools package. Often contains comments about changes to hosting addresses, information about read/write permission, or quirks about working with specific data.
A float or int value for setting the tracer-chosen default 2D viewer window zoom level when constructing programmatically-generated neuroglancer links.
A float or int value for setting the tracer-chosen default 3D viewer window zoom level when constructing programmatically-generated neuroglancer links.
A list of 4 float or int values for setting the tracer-chosen default 3D viewer window angle when constructing programmatically-generated neuroglancer links.
Note
If a value of [0,0,0,0] is ever passed it will break the ability to rotate the 3D view by clicking + dragging. This is believed to be because the mechanism of rotation multiplies the numbers, and 0 x 0 = 0. If such a link is generated, pressing z while hovering the mouse over the 3D view window should snap the view to [0,0,0,1] and resolve the bug.
The dimensions in nanometers used by the datastack's default viewer for a single voxel. For a more detailed description, see the glossary entry. E.g. a viewer_res value of [4, 4, 45] means each voxel is 4nm x 4nm x 45nm in the x, y, and z dimensions respectively.
The hosting address of the version of neuroglancer this datastack is built to work with. Often used as a base when programmatically constructing state links.
A list of point coordinates for the tracer-chosen default focal point used when generating neuroglancer links programmatically. Often close to the center of the whole stack mesh.
The overall x, y, and z dimensions in voxels of the volume for the datastack's segmentation. Note that these coordinates are in voxels, not nanometers. To convert to nanometers, multiply the volume_size numbers by their viewer_res counterparts.
The minimum coordinate of the datastack. Usually [0,0,0], but some datastacks may use an offset minimum for various reasons.
The maximum coordinate of the datastack.
The coordinates of the centerpoint of the datastack.
The address where the volume containing the overall mesh encompassing a whole datastack is hosted, if one exists. These are usually formatted as precomputed static meshes.
Some datastacks may also have their own unique config entries to suit the needs of the project. Common examples are host urls for the segmentations or meshes of other datastacks that have been aligned for comparison purposes, custom mesh hosting urls for specific structures like nerve bundles, or precomputed annotation layers for synapses, nuclei, organelles, or other structures.
The code below gets the config dictionary for the brain_and_nerve_cord datastack.
INPUT:
import tracertools as tt
config = tt.get_config(
datastack = "brain_and_nerve_cord",
)
print(config)
OUTPUT:
{
"alignment_display_name": "BANC",
"alignment_cave_id": 9,
"alignment_description" : 'The BANC (said "the bank") is the Brain And Nerve Cord, a GridTape transmission electron microscopy dataset of a female adult Drosophila melanogaster\'s entire central nervous system. Visit https://banc.community for more information.',
"alignment_name": "brain_and_nerve_cord",
"cell_info_table_format" : "cell_std",
"cell_info_table_name" : "cell_info",
"dataset_name": "BANC",
"datastack_description": None,
"image_source" : "precomputed://gs://seunglab_lee_fly_cns_001_alignment/aligned/v0",
"local_server" : "https://cave.fanc-fly.com",
"neuropil_mesh_source" : None,
"proofreading_table_format" : "proof_std",
"proofreading_table_name" : "backbone_proofread",
"seg_source" : "graphene://middleauth+https://cave.fanc-fly.com/segmentation/table/wclee_fly_cns_001",
"shortlink_server" : None,
"skeleton_source" : "precomputed://https://cave.fanc-fly.com/skeletoncache/api/v1/brain_and_nerve_cord/precomputed/skeleton",
"soma_table_format" : None,
"soma_table_name" : None,
"swamp_mesh_source" : "https://c10s.pni.princeton.edu/tracers/swamps/banc/main|neuroglancer-precomputed:",
"swamp_seg_ids": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
"synapse_table_format": "syn_std",
"synapse_table_name": "synapses_v2",
"tt_notes": None,
"viewer_2d_zoom" : 4.12,
"viewer_3d_angle" : [0, 1, 0, 0],
"viewer_3d_zoom" : 360849,
"viewer_res" : [4, 4, 45],
"viewer_site" : "https://spelunker.cave-explorer.org/",
"viewer_start_coords" : [125563, 118181, 2850],
"volume_size" : [262144, 294912, 7010],
"volume_min_coord" : [0, 0, 0],
"volume_max_coord" : [262143, 294911, 7009],
"volume_center_coord": [131027, 147460, 3505],
"whole_stack_mesh_source" : "precomputed://gs://lee-lab_brain-and-nerve-cord-fly-connectome/region_outlines",
"manc_seg_source": "precomputed://gs://lee-lab_brain-and-nerve-cord-fly-connectome/imported_meshes/manc_v1.2.1_meshes_elastix_tpsreg_240721",
}
Note
This output was generated on 2026/10/12 and may look different when run in the future. As you can see, not all the attributes have values for any given datastack. This will vary from stack to stack and is based on what the publisher has made available.