The evolution of Big Data in neuroscience and neurology

Dipietro, Laura; Gonzalez-Mego, Paola; Ramos-Estebanez, Ciro; Zukowski, Lauren Hana; Mikkilineni, Rahul; Rushmore, Richard Jarrett; Wagner, Timothy

doi:10.1186/s40537-023-00751-2

Journal of Big Data

Table 3 Sample of Connectome Studies and Evolving Big Data Use

From: The evolution of Big Data in neuroscience and neurology

Refs	Date	Author	Vol	Var	Vel	Ver	Val
[66]	1986	White	Imaging: “302 Neurons”, “5000 chemical synapses, 2000 neuromuscular junctions and 600 gap junctions”	Anatomical EM studies of a Nematode nervous system	F	M	P
[242]	1993	Young	Tabulated: 72 areas with connections coded via 0 no, 1 one-way, and 2 two-way connections	Neuroanatomical literature review (Macaque cortical areas)	F	M	P
[67]	1995	Scannell	Tabulated: 1139 reported corticocortical connections between 65 cortical areas	Neuroanatomical literature review (Feline cortical areas)	F	M	P
[243]	2001	Stephan	Tabulated: 270 papers– > 4723 Brain Sites with connection data from 0 to 3 in strength to build CoCoMac database	Literature review of tracer studies in Macaque	F	Mix	P
[31, 244]	2003	Bota	Tabulated: Multiple Data Set Types (e.g., Multiple Rat connectomes (50,000 + connectivity reports each))	Variety across data types and organisms (Rat & Macaque)	F	Mix	P
[245]	2010	Modha	Tabulated: Focused on 383 regions “spanning cortex, thalamus, and basal ganglia”; models “6,602 directed long-distance connections”	Collation of 410 Macaque tracer studies from CoCoMac	F	Mix	P
[246]	2011	Bock	Imaging: 1500 cell bodies of visual cortex with reconstruction of 245 synapses originating from 10 functionally characterized pyramidal neurons	Anatomical EM and Functional 2P imaging mouse visual cortex	F	M	P
[247]	2011	Briggman	Imaging: 634 neuronal cell bodies, with 25 Directionally Sensitive On–Off Cells in retina	Mouse Anatomical EM, Functional 2P, and visual stimulation results	F	M	P
[72]	2011	van den Heuvel	Imaging: DTI (n = 21) focused on 12 strongly interconnected bihemispheric hub regions	DTI & random attack simulation assess connection weight from 21 Humans	F	A	C
[230, 231, 232]	2011	Van Essen, Glasser	Imaging and clinical data: Over 1000 subjects (healthy young adult 22–35), over 1000 Aging adults (36–100 +), etc. following protocols of HCP	Multimodal imaging, clinical, genetic, biospecimens for 1000’s subjects	O	A	C
[248]	2012	Harriger	Tabulated: 410 studies from CoCoMac—> whole-brain connection matrix (352 regions) & cortical connectome for 242 regions and 4090 projections	Collation of 410 Macaque tracer studies from CoCoMac	F	A	P
[249]	2012	Jarrell	Imaging: 144 neurons, 64 muscles, and 1 gonad (at synaptic level)	Nematode EM, Simulation and Correlation with past experiments	F*	DML	P
[250]	2013	Takemura	Imaging: 379 neurons and 8,637 chemical synaptic contacts of Optic Medulla (focused on motion detection cells)	Anatomical EM studies from Fruit Fly	F	Mix	P
[251]	2014	Markov	Imaging: “29 of the 91 areas of the macaque cerebral cortex revealed 1615 interareal pathways”	Retrograde tracer injection studies and simulations from Macaque	F	A	P
[252]	2014	Ingalhalikar	Imaging: Structural connectome (“95 regions of interest (Regions of Interest; 68 cortical and 27 subcortical regions)” from 949 DTIs	Human DTI Imaging (Male vs. Female, 428 Male and 521 Female)	F	A	C
[253]	2014	Deligianni	Imaging: “Simultaneous resting-state EEG-fMRI was acquired from 17 adult volunteers”	Human (n = 17) EEG and fMRI comparisons	F	A	P
[71]	2015	Ohyama	Imaging: Electron Microscopy spans 10,000 neuron nervous system, but reconstructed multisensory circuit supporting synergy	Fruit Fly Anatomical EM, Behavioral, Optogenetics, Physiological Data	F	Mix	P
[254]	2015	Bota	Tabulated: 16,000 BAMS database reports of histologically defined axonal connections to assess cognition 923 rat cortical association connections	Collation of histology studies from 16,000 rats	F*	M	P
[255]	2016	Ryann	Imaging: 177 CNS neurons, 6618 synapses (including 1772 neuromuscular junctions, augmented by 1206 gap junctions)	Anatomical EM (but includes 2P coregistered data for future use) from Tadpole larva)	F	Mix	P
[256]	2017	Hildebrand	Imaging: Complete larval zebrafish brains but reconstructions focused on 2589 myelinated axons	Anatomical EM and Functional 2P from zebrafish larva	F	Mix	P
[257]	2017	Vishwanthan	Imaging: 2967 somata identified with “22 integrator neurons” “and annotated the pre- and” postsynaptic locations reconstructed	Anatomical EM and Functional 2P from zebrafish larva	F	Mix	P
[33]	2018	Zheng	Imaging: Electron Microscopy spans 100,000 neuron nervous brain, but reconstruction centered on the mushroom body (MB)	Fruit Fly Anatomical EM reconstructions with light microscopy databases	F*	Mix	P
[258]	2019	Ardesch	Imaging: DTI Humans (n = 57) and chimpanzees (n = 20), with analysis focused on rich club organization from 36 areas per hemisphere [72 in total] for both species	Human vs. non Human Primate DTI	F	Mix	P
[74]	2019	Van Essen	Imaging: Differs across species	Human (MRI), Non-Human Primate (MRI), Mouse (tracer) imaging	F	Mix	P
[7]	2020	Scheffer	Imaging: Around 25,000 neurons, with most “clustered and named”, and approximately 20 million synapses mapped for the central brain circuits (assuming bilateral symmetry)	Fruit Fly Anatomical EM studies and neural simulations	F*	Mix	P
[70]	2020	Wanner	Imaging: 1003 neurons of Olfactory Bulb (Mitral cells (n = 745), interneurons, (n = 254), and “atypical projection neurons” (n = 4)	Anatomical EM, Functional 2P, and Simulation from zebrafish larva	F	Mix	P
[259]	2021	Ashaber	Imaging and Behavioral: Recorded from 25 neurons simultaneously, but focused on reconstruction of Explore Dorsal Excitor motor neuron DE-3 and 531 synapses of the cell	Anatomical EM, Functional Voltage Sensitive Dye, Behavioral Observation, X-ray tomography from Medicinal Leech	F	Mix	P
[260]	2021	Scholl	Imaging and stimulation data: Imaging and stimulation data: “155 visually responsive” “synapses imaged in vivo on 23 dendritic segments from 5 cells”	Anatomical EM, Functional 2P, and visual stimulation results from Ferrets	F	Mix	P
[261]	2021	Brittin	Imaging: 2 complete connectomes (adult and larva)	Nematode Adult and Larva Anatomical EM	F	Mix	P
[262]	2021	Sorrentino	Imaging: Structural connectomes of 58 healthy adults [26 females, 32 males]	DTI and MEG combination (MEG better temporal resolution) from Humans	F	Mix	P
[15]	2021	Demro	247 participants completed the study as of publication date following data collection protocols of HCP (multimodal imaging) and additional clinical/behavioral/cognitive data	Data as defined by HCP project, plus additional clinical, behavioral, and cognitive metrics in 247 psych patients	O	Mix	C
[263]	2022	Scholl	Imaging and stimulation data: Characterized 5923 visually responsive dendritic spines from 35 cells with focus on 28 binocular cells	Anatomical EM, Functional 2P, visual stimulus, and simulation	F	Mix	P
[13]	2022	Bethlehem	Imaging: MRI repository “aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post and conception to 100 years of age”	Longitudinal Information from 101,457 human participants (including modeled simulations)	O	Mix	C
[264]	2022	Chen	Imaging: “Resting-state functional connectivity (rs-fcMRI) data from 1416 healthy adults” (“whole brain into 300 parcels, including 27 cerebellar areas and 273 cerebral areas”)	rs-fcMRI data combined with Markov model to ascertain functional connectivity from 1416 healthy adult humans	F	A	C

We have classified the experiments with the classic 5 V’s definition. However, certain categories are not clearly defined in the review of prospective, retrospective, and data collation studies. For Volume (Vol): We focused on volume of Imaged Structures for histology-based Imaging (e.g., Anatomical EM studies) and the size of patient cohorts and experimental data for clinical studies. We chose this method as there is not a clear standard in reporting digital data sizes across the literature. For Variety (Var): We indicate the different data and specimen types. For Velocity (Vel): We reported the data Velocity as either ‘F’ for Fixed Studies (analyzing data from databases or studies which are no longer acquiring data) or ‘O’ for Ongoing studies (analyzing data from databases or clinical studies that are still acquiring data, although it should be noted that the reported results of the studies are based on analysis of a fixed data set with the noted volume at the time of the publication). We discuss this further in the text, but implemented this simplified standard given: 1. Few studies report data in a manner that allows one to calculate data Velocity acquisition and processing (e.g., for clinical trials, which are dependent on ‘unpredictable’ patient recruitment rates and Data Acquisition velocities are often not clearly reported), 2. For the multimodal nature of data in the above studies there is not a standard of how velocity should be reported (e.g., Scheffer reported “over 50 person-years of proofreading effort over ≈2 calendar years” transforming 20 TB of raw data into 26 MB useable network diagrams for the Imaging “25,000 neurons. most of which were clustered and named” with “about 20 million chemical synapses” for an estimated speed of 400,000 synapses/person year or a transformation speed of 0.4 TB raw data/person year). Where any type of Velocity information is given, and a velocity calculation can be made, it is provided in the Additional file 1: Table S3 (and noted herein with a *). For Veracity (Ver): M Manual verification; A Data verified through automated analytical process (e.g., AI, statistical methods), Mix Automated Analytical and Manual (or semi-automated). However, all experimental data veracity is dependent on the methodological limitations of the core studies, thus we also provide examples of variability or error in the Additional file 1: Table S3 (if no explicit assessment of data Veracity is outlined in the publication or the data does not come from a validated database (e.g., primary research data), the study is just marked DML Dependent on Methodological Limitations and expanded upon in the Additional file 1: Table). For Value (Val): As neither study costs are disclosed, health economics assessments completed, nor a monetary cost assigned in the sale or purchase of any of the above data sets, we simply report on the study as having “P” for Preclinical or “C” for Clinical value dependent on the study species and Data Use. The limitations to these definitions and study information availability are described in the text. For Year we indicate the year of the earliest publication. Ref Reference

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