FlyBrainLab Datasets

This repository contains information regarding the FlyBrainLab Datasets (version, source, loading scripts, etc.) Here, we provide a summary of the datasets available under NeuroArch database, and links to the preloaded database backup files that can be used to restored the databases. Detailed instructions for loading these databases from scratch are provided in the individual folders and/or notebooks.

FlyCircuit | Hemibrain | Larva L1EM | Medulla 7 Column | MANC | FlyWire | FIB19 Optic Lobe

FlyCircuit Dataset [1]

FlyCircuit Ver.	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
1.2	0414129	flycircuit1.2_na_v2.0.1_backup.zip	Link	06/17/2022 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/flycircuit admin admin; restore database /path/to/flycircuit1.2_na_v2.0.1_backup.zip"

Hemibrain Dataset [2]

Original data licensed under CC-BY 4.0.

Hemibrain Ver.	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
1.0.1	73d6b81	hemibrain1.0.1_na_v1.0_backup.zip	Link	01/27/2021 Release Notes	Link
1.1	73d6b81	hemibrain1.1_na_v1.0_backup.zip	Link	01/27/2021 Release Notes	Link
1.2	0414129	hemibrain1.2_na_v2.0.1_backup.zip	Link	06/17/2022 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/hemibrain admin admin; restore database /path/to/hemibrain1.2_na_v2.0.1_backup.zip"

Larva L1EM [3]

Original data licensed under CC-BY-SA 4.0.

L1EM Ver.	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
1.0	0414129	l1em1.0_na_v2.0.1_backup.zip	Link	06/17/2022 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/l1em admin admin; restore database /path/to/l1em1.0_na_v2.0.1_backup.zip"

Medulla 7 Column Dataset [4]

Original data licensed under BSD 3. Neuron Skeleton data from ConnectomeHackathon2015 and is licensed under the Open Data Commons Attribution License.

Medulla Ver.	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
fib25	0414129	medulla7column_fib25_na_v2.0.2_backup.zip	Link	07/06/2022 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/medulla admin admin; restore database /path/to/medulla7column_fib25_na_v2.0.2_backup.zip"

Male Adult Nerve Cord Dataset [5]

Original data licensed under CC-BY.

MANC Ver.	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
1.0	1126f43	manc1.0_na_v1.0.0_backup.zip	Link	08/16/2023 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/manc admin admin; restore database /path/to/manc1.0_na_v1.0.0_backup.zip"

FlyWire Dataset [6]

Original data licensed under CC-BY-NC.

FlyWire Snapshot	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
630	1126f43	flywire630_na_v1.0.0_backup.zip	Link	08/16/2023 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/flywire admin admin; restore database /path/to/flywire630_na_v1.0.0_backup.zip"

FIB19 Optic Lobe Dataset [7]

Original data licensed under CC-BY.

FlyWire Snapshot	NeuroArch Ver.	Download Link	Loading Script	Last Update	NeuroNLP
1.0	1126f43	fib19_1.0_na_v1.0.0_backup.zip	Link	08/16/2023 Release Notes	Link

To load the database in OrientDB, use the following command (and replace /path/to in two places to the directory of the orientdb and the downloaded zip file, respectively):

/path/to/orientdb/bin/console.sh "create database plocal:../databases/fib19 admin admin; restore database /path/to/fib19_1.0_na_v1.0.0_backup.zip"

References

1. Ann-Shyn Chiang et al., Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution, Current Biology 2011, 21(1), pp.1-11. DOI.
2. Louis K. Scheffer et al., A connectome and analysis of the adult Drosophila central brain. eLife 2020;9:e57443. DOI.
3. Ohyama T. et al., A multilevel multimodal circuit enhances action selection in Drosophila. Nature. 2015. DOI.
4. Takemura S. et al., Synaptic circuits and their variations in the fly medulla. Proceedings of the National Academy of Sciences. 2015, 112 (44) 13711-13716. DOI.
5. Shin-ya Takemura et al., A Connectome of the Male Drosophila Ventral Nerve Cord bioRxiv, 2023.06.05.543757, 2023. DOI.
6. Sven Dorkenwald et al., Neuronal wiring diagram of an adult brain bioRxiv 2023.06.27.546656, 2023 DOI.
7. Kazunori Shinomiya et al., Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain. eLife 8:e40025, 2019. DOI.