NDLI: SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

Please wait, while we are loading the content...

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

Content Provider	PubMed Central
Author	Shi, Bitao Bourne, Jennifer Harris, Kristen M.
Abstract	Serial section electron microscopy (ssEM) is rapidly expanding as a primary tool to investigate synaptic circuitry and plasticity. The ultrastructural images collected through ssEM are content rich and their comprehensive analysis is beyond the capacity of an individual laboratory. Hence, sharing ultrastructural data is becoming crucial to visualize, analyze, and discover the structural basis of synaptic circuitry and function in the brain. We devised a web-based management system called SynapticDB (http://synapses.clm.utexas.edu/synapticdb/) that catalogues, extracts, analyzes, and shares experimental data from ssEM. The management strategy involves a library with check-in, checkout and experimental tracking mechanisms. We developed a series of spreadsheet templates (MS Excel, Open Office spreadsheet, etc) that guide users in methods of data collection, structural identification, and quantitative analysis through ssEM. SynapticDB provides flexible access to complete templates, or to individual columns with instructional headers that can be selected to create user-defined templates. New templates can also be generated and uploaded. Research progress is tracked via experimental note management and dynamic PDF forms that allow new investigators to follow standard protocols and experienced researchers to expand the range of data collected and shared. The combined use of templates and tracking notes ensures that the supporting experimental information is populated into the database and associated with the appropriate ssEM images and analyses. We anticipate that SynapticDB will serve future meta-analyses towards new discoveries about the composition and circuitry of neurons and glia, and new understanding about structural plasticity during development, behavior, learning, memory, and neuropathology.
Related Links	http://dx.doi.org/10.1007/s12021-010-9088-4
Ending Page	57
Page Count	19
Starting Page	39
File Format	PDF
ISSN	15392791
e-ISSN	15590089
Journal	Neuroinformatics
Issue Number	1
Volume Number	9
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-03-01
Access Restriction	Open
Rights Holder	Springer-Verlag
Subject Keyword	Software Neuroscience(all) Information Systems Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Neuroscience Information Systems Software

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

A Community Spring For Neuroscience Data Sharing

Domain-Specific Data Sharing in Neuroscience: What do we have to learn from each other?

Sharing Heterogeneous Data: The National Database for Autism Research

A Fast Method for the Segmentation of Synaptic Junctions and Mitochondria in Serial Electron Microscopic Images of the Brain

NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks

Semi-automated Neuron Boundary Detection and Nonbranching ProcessSegmentation in Electron Microscopy Images

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

Similar Documents

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy

Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

A Community Spring For Neuroscience Data Sharing

Domain-Specific Data Sharing in Neuroscience: What do we have to learn from each other?

Sharing Heterogeneous Data: The National Database for Autism Research

A Fast Method for the Segmentation of Synaptic Junctions and Mitochondria in Serial Electron Microscopic Images of the Brain

NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks

Semi-automated Neuron Boundary Detection and Nonbranching ProcessSegmentation in Electron Microscopy Images

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy