A multiscale brain map derived from whole-brain volumetric reconstructions

README.txt

Brittin, C. A. , Cook, S. J., Hall, D.H., Emmons, S. W., Cohen. N. A multiscale brain map derived from whole-brain volumetric reconstructions. Nature (2021) [paper].

This archive provides source volumetric and synaptic data for Brittin et al. (2021).
Associated software repositories:
    * parsetrakem2 -- https://github.com/cabrittin/parsetrakem2
    * elegansbrainmap --  https://github.com/cabrittin/elegansbrainmap

Alternatively, the data is available at https:/www.wormwiring.org

Summary of Brittin et al. (2021):

Animal nervous system organization is crucial for all body functions and its disruption can manifest in severe cognitive and behavioral impairment. This organization relies on features across scales, from nano-level localization of synapses, through multiplicities of neuronal morphologies and their contribution to circuit organization, to the high level stereotyped connections between different regions of the brain. The sheer complexity of this organ means that to date, we have yet to reconstruct and model the structure of a complete nervous system that is integrated across all these scales. Here, we present a complete structure-function model of the nematode C. elegans main neuropil, the nerve ring, which we derive by integrating the volumetric reconstruction from two animals with corresponding synaptic and gap junctional connectomes. Whereas previously the nerve ring was considered a densely packed tract of neural processes, we uncover internal organization and show how local neighborhoods spatially constrain and support the synaptic connectome. We find that the C. elegans connectome is not invariant, but that a precisely wired core circuit is embedded in a background of variable connectivity, and propose a corresponding reference connectome for the core circuit. Using this reference, we show that the architecture of the C. elegans brain can be viewed as a modular network that supports sensory computation and integration, sensory-motor convergence, and brain-wide coordination. These findings point to scalable and robust features of brain organization that are likely universal across phyla.

Updates:

2021-05-14: v1.1.0: added files adult_volumes.tar.bz2 and l4_volumes.tar.bz2 which have the wavefront (.obj and .mtl) files for each neuron volume. 

Tar, bzipped files included:
* jsh_trakem2_mipmaps.tar.bz2
* n2u_trakem2_mipmaps.tar.bz2
    - n2u_trakem2_mipmaps.tar.bz2.aa
    - n2u_trakem2_mipmaps.tar.bz2.ab
    - n2u_trakem2_mipmaps.tar.bz2.ac
    - n2u_trakem2_mipmaps.tar.bz2.ad
    - n2u_trakem2_mipmaps.tar.bz2.ae
    - n2u_trakem2_mipmaps.tar.bz2.af
    - n2u_trakem2_mipmaps.tar.bz2.ag
    - n2u_trakem2_mipmaps.tar.bz2.ah
    - n2u_trakem2_mipmaps.tar.bz2.ai
    - n2u_trakem2_mipmaps.tar.bz2.aj

* jsh_trakem2_segmentations.tar.bz2
* n2u_trakem2_segmentations.tar.bz2
* adjacency.tar.bz2
* databases.tar.bz2
* reference_graphs.tar.bz2
* population_spatial_models.tar.bz2
* jsh_process_structures.tar.bz2
* n2u_process_structures.tar.bz2
* brainmap.tar.bz2

Uncompress and see associated README files for further details.

On linux, to uncompress
tar -xvjf __file_name_.tar.bz2

#### jsh_trakem2_mipmaps.tar.bz2 ####
Mipmaps files for the L4 TrakEM2 data (see https://imagej.net/TrakEM2). Requires FIJI for viewing (https://imagej.net/Fiji). These files are required to view TrakEM2 data. The TrakEM2 xml files should be in the same directory as the (uncompressed) mipmaps directory. The xml file can then be opened in FIJI.   

#### n2u_trakem2_mipmaps.tar.bz2 ####
Mipmaps files for the adul TrakEM2 data (see https://imagej.net/TrakEM2). Requires FIJI for viewing (https://imagej.net/Fiji). These files are required to view TrakEM2 data. The TrakEM2 xml files should be in the same directory as the (uncompressed) mipmaps directory. The xml file can then be opened in FIJI.   

Due to upload limitations, we have split this file into ten <1GB files.
    - n2u_trakem2_mipmaps.tar.bz2.aa
    - n2u_trakem2_mipmaps.tar.bz2.ab
    - n2u_trakem2_mipmaps.tar.bz2.ac
    - n2u_trakem2_mipmaps.tar.bz2.ad
    - n2u_trakem2_mipmaps.tar.bz2.ae
    - n2u_trakem2_mipmaps.tar.bz2.af
    - n2u_trakem2_mipmaps.tar.bz2.ag
    - n2u_trakem2_mipmaps.tar.bz2.ah
    - n2u_trakem2_mipmaps.tar.bz2.ai
    - n2u_trakem2_mipmaps.tar.bz2.aj

On linux, the files can be recombined with
cat n2u_trakem2_mipmaps.tar.bz2.a* | bunzip2 | tar -xvf -

Which gives a mipmaps and masks directy. Now make the directory
mkdir trakem2.1370550189338.1671964219.113318782

and move the mipmaps and masks to the new directory
mv trakem2.mipmaps trakem2.1370550189338.1671964219.113318782/
mv trakem2.masks trakem2.1370550189338.1671964219.113318782/

##### jsh_trakem2_segmentations.tar.bz2 #####
Segmented L4 dataset to be used in conjuction with the mipmaps files for the L4 TrakEM2 (jsh_trakem2_mipmaps.tar.bz2).

#### n2u_trakem2_segmentations.tar.bz2 ####
Segmented adult dataset to be used in conjuction with the mipmaps files for the L4 TrakEM2 (n2u_trakem2_mipmaps.tar.bz2).

####  adjacency.tar.bz2 ####
Adjacency data for L4 and adult data sets extracted from TrakEM2 file.  

#### databases.tar.bz2 ###
Membrane contact data in the form of sql databases which is the primary data source for the analysis code used in this paper, see https://github.com/cabrittin/elegansbrainmap.

##### reference_graphs.tar.bz2 #####
Reference graphs in graphml format, which serve as direct input elegancebrainmap analysis package. For ASCII file format of the same data see Supplementary Information 3 of Brittin et al. (2021).

##### population_spatial_models.tar.bz2 #####
Results from the population spatial models for Fig. 1c,d, Extended Data Fig. 5,6 and Supplementary Information 4 in Brittin et al. (2021). Files are in numpy binary format, see elegancebrainmap repo for details of usage.

#### jsh_process_structures.tar.bz2 ####
Support TrakEM2 files for L4 process structures for all cells described in Fig 3d-g, Extended Data Fig. 8 and Supplementary Information 4. Only segmentation files for the left cell in each cell class is provided. Segmentation files for the right cell can be generated using parsetrakem2.  Note that in the manuscript only L4 processes are shown.  

#### n2u_process_structures.tar.bz2 ####
Support TrakEM2 files for adult process structures for all cells described in Fig 3d-g, Extended Data Fig. 8 and Supplementary Information 4. Only segmentation files for the left cell in each cell class is provided. Segmentation files for the right cell can be generated using parsetrakem2.

##### brainmap.tar.bz2 #####
Cytoscape and source graph files used to generate brain map images (Fig. 4, Extended Data Fig 9,10 in Brittin et al. 2021).