Long-range axonal projections analyses of the mouse brain

Accompanying data and analyses of the article "Generating brain-wide connectome using synthetic axonal morphologies". The code to reproduce the figures is available at this repository.

Main contents:

SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, Peng et al. 2021, Winnubst et al. 2019) after morphology-workflows Repair post-processing steps.

atlas: atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)

out_a_p: output of the axonal projection* anaylsis and clustering on the 3601 morphologies of the dataset.

axon_lengths_12.csv, axon_terminals_12.csv: the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.

clustering_output.csv: output of the GMM clustering.

config_a_p.cfg: configuration file used to produce this analysis, with running the axonal projection code.

circuit: contains files describing the circuit synthesized with Blue Brain's circuit-build*.

bioname: parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).

sonata: files that contain nodes and edges of the circuit.

auxiliary: various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with Voxcell.

conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with ConnectomeUtilities.Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.

local_axons: biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.

synthesized_MOp5_LRAs: 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. 

out_a_p_synth_MOp5: axonal projection analysis of the synthesized MOp5 axons.

synthesized_isocortex_cells: all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with MorphIO.

synthesized_isocortex_LRAs: 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. 

Additional files:

flatmap_both.nrrd: file used to generate a flat map visualization of the mouse isocortex, shown in the article.

config_a_s.cfg: configuration file used to synthesize the long-range axons with the axon-synthesis* code.

target_pts: tufts common ancestors for the synthesized MOp5 axons.

brain_atlas.zip: a lightweight version of the mouse brain atlas for the synthesis code example.

*These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.