Difference between revisions of "FlyBase:Neuroscience"

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=Popular Resource Categories=
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|style="text-align: center; padding: 15px;"| <big>[[FlyBase:External_Resources|All Resources]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Stocks|Stocks]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Antibodies|Antibodies]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Images|Images]]</big>||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Neuroscience|Neuroscience]]</big>
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|style="text-align: center; padding: 15px;"| <big>[[FlyBase:External_Resources|All Resources]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:ScRNA-Seq|ScRNA-Seq]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Stocks|Stocks]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase: Antibodies|Antibodies]]</big>||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Neuroscience|Neuroscience]]</big>
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|style="text-align: center; padding: 20px;"| <big>[[FlyBase:Model_Organism_Databases|Model Organism<br/> Databases]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Images|Images]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Maps|Maps]]</big> ||style="text-align: center; padding: 20px;"| <big>[http://www.flyrnai.org/tools/protocols/web/ Protocols]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Papers_with_technical_advances|Papers with<br/> Technical Advances]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:GSEA|Gene Set<br/> Enrichment Tools]]</big>
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= Neuroscience Image Databases =
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= Databases of expression, anatomy and physiology=
  
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [http://brainbase.imp.ac.at BrainBase] ||style="background: #efefef;"| Database of images and annotations of expression for VT and enhancer trap GAL4 lines||style="white-space: nowrap; background: #efefef;"|Barry Dickson Lab<br/> formerly at Institute of Molecular Pathology<br/>Vienna, Austria<br/ >Biomedical Visualization Group<br />VRVis<br/ >Vienna, Austria
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|style="background: #efefef;"| [https://flweb.janelia.org/cgi-bin/flew.cgi FlyLight GAL4 and LexA lines] ||style="background: #efefef;"| Database of expression patterns of GAL4 and LexA driver lines from Janelia Research Campus||style="background: #efefef;"| Janelia FlyLight Project Team<br/>Gerry Rubin Lab<br />James Truman Lab<br />Richard Mann Lab<br/>Chris Doe Lab<br />Janelia Research Campus<br />Virginia, USA
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| [http://fruitfly.inf.ed.ac.uk/braintrap/ BrainTrap] || Database with expression of protein trap lines in the adult brain || [http://dx.doi.org/10.1093/database/baq005 Knowles-Barley et al., 2010]
 
 
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|style="background: #efefef;"|[http://ndb.flybrain.org FlyBrain Neuron NDB] ||style="background: #efefef;"|Database of neuron, strain, antibody and brain regions data. ||style="background: #efefef;"| Laboratory of Structural Information<br />Institute of Molecular and Cellular Biosciences<br />The University of Tokyo<br/>Tokyo, Japan
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| [https://splitgal4.janelia.org/cgi-bin/splitgal4.cgi FlyLight Split GAL4 lines] ||Database of expression patterns of Split GAL4 lines from Janelia Research Campus||Janelia FlyLight Project Team<br/>Gerry Rubin Lab<br />Janelia Research Campus<br /> Virginia, USA
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| [http://www.flycircuit.tw/ FlyCircuit] || Database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neuron images in the adult brain|| [http://dx.doi.org/10.1016/j.cub.2010.11.056 Chiang et al., 2011]
 
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|style="background: #efefef;"| [http://flweb.janelia.org/cgi-bin/flew.cgi FlyLight GAL4 lines] ||style="background: #efefef;"| Database of expression patterns of GAL4 and LexA driver lines from Janelia Research Campus||style="background: #efefef;"| Janelia FlyLight Project Team<br/>Gerry Rubin Lab<br />James Truman Lab<br />Richard Mann Lab<br/>Chris Doe Lab<br />Janelia Research Campus<br />Virginia, USA
 
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| [http://splitgal4.janelia.org/cgi-bin/splitgal4.cgi FlyLight Split GAL4 lines] ||Database of expression patterns of Split GAL4 lines from Janelia Research Campus||Janelia FlyLight Project Team<br/>Gerry Rubin Lab<br />Janelia Research Campus<br /> Virginia, USA
 
 
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|style="background: #efefef;"| [http://www.fly-trap.org/ Fly Trap] ||style="background: #efefef;"| Database of classical P(GAL4) enhancer traps imaged in head sections ||style="background: #efefef;"|Armstrong Lab<br/> University of Edinburgh<br/>Edinburgh, UK
 
|style="background: #efefef;"| [http://www.fly-trap.org/ Fly Trap] ||style="background: #efefef;"| Database of classical P(GAL4) enhancer traps imaged in head sections ||style="background: #efefef;"|Armstrong Lab<br/> University of Edinburgh<br/>Edinburgh, UK
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [www.virtualflybrain.org Virtual Fly Brain]||style="background: #efefef;"| Interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of ''Drosophila melanogaster'' ||style="background: #efefef;"| [http://dx.doi.org/10.1093/bioinformatics/btr677 Milyaev et al., 2012]
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|style="white-space: nowrap; background: #efefef;"| [http://www.virtualflybrain.org Virtual Fly Brain]||style="background: #efefef;"| Interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of ''Drosophila melanogaster'' ||style="background: #efefef;"| [http://dx.doi.org/10.1093/bioinformatics/btr677 Milyaev et al., 2012]
 
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| [https://braingazer.org/ BrainGazer] || Desktop interactive tool for advanced visualization and exploration of neural circuit data||style="white-space: nowrap;"| [http://dx.doi.org/10.1109/TVCG.2009.121 Bruckner et al., 2009]
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| [https://natverse.org/nat.flybrains/ Bridging registrations] || This site provides the tools to transform image data from one template brain (adult ''Drosophila'') to another, using a bridging registration. ||[http://dx.doi.org/10.1101/006353 Manton et al., 2014]
 
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| [http://jefferislab.org/si/nblast/ NBLAST] || Tool to search for similar neurons by morphology and location||style="white-space: nowrap;"| [http://dx.doi.org/10.1101/006346 Costa et al., 2014]
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| style="white-space: nowrap; background: #efefef;"|[http://jefferislab.org/si/nblast/ NBLAST] || style="white-space: nowrap; background: #efefef;"|Tool to search for similar neurons by morphology and location||style="white-space: nowrap; background: #efefef;"| [http://dx.doi.org/10.1101/006346 Costa et al., 2014]
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|style="background: #efefef;"| [http://jefferislab.org/si/bridging/www/ Bridging registrations] ||style="background: #efefef;"| This site provides the tools to transform image data from one template brain (adult ''Drosophila'') to another, using a bridging registration. ||style="background: #efefef;"|[http://dx.doi.org/10.1101/006353 Manton et al., 2014]
 
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| [http://ndb.flybrain.org Braincode] || Automated segmentation of the Drosophila brain to identify "functional units"||style="white-space: nowrap;"| [http://dx.doi.org/10.1101/032292  Panser et al., 2015]
 
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS]||style="background: #efefef;"| Description of embryonic and larval sensory organs of ''D. melanogaster'' that are located in abdominal segments A1-A7 ||style="background: #efefef;"| [http://dx.doi.org/10.1186/1471-213X-5-4 Orgogozo and Grueber, 2005]
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| [https://www.sciencedirect.com/science/article/pii/S0012160697986607?via%3Dihub Embryonic and larval neuroblasts and lineages] || Interactive maps of the embryonic and larval neuroblasts and lineages||style="white-space: nowrap;"| Christof Rickert<br />University of Mainz<br />Mainz, Germany
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| [http://www.genetik.biologie.uni-mainz.de/106.php Embryonic and larval neuroblasts and lineages] || Interactive maps of the embryonic and larval neuroblasts and lineages||style="white-space: nowrap;"| Christof Rickert<br />University of Mainz<br />Mainz, Germany
 
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| [http://www.ice.mpg.de/ext/suppl-rybak.html Adult antennal lobe 3D model] || 3D model of adult antennal lobe||style="white-space: nowrap;"| [http://dx.doi.org/10.1002/cne.23966 Rybak et al., 2016]
 
 
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|style="white-space: nowrap; background: #efefef;"| [http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS]||style="background: #efefef;"| Description of embryonic and larval sensory organs of ''D. melanogaster'' in abdominal segments A1-A7 ||style="background: #efefef;"| [http://dx.doi.org/10.1186/1471-213X-5-4 Orgogozo and Grueber, 2005]
 
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Latest revision as of 21:19, 11 October 2023

Popular Resource Categories

All Resources CRISPR ScRNA-Seq RNAi Stocks Antibodies Neuroscience
Model Organism
Databases		 Images Maps Protocols Papers with
Technical Advances		 Gene Set
Enrichment Tools

Databases of expression, anatomy and physiology

Resource Description Author/Source
FlyLight GAL4 and LexA lines Database of expression patterns of GAL4 and LexA driver lines from Janelia Research Campus Janelia FlyLight Project Team
Gerry Rubin Lab
James Truman Lab
Richard Mann Lab
Chris Doe Lab
Janelia Research Campus
Virginia, USA
FlyLight Split GAL4 lines Database of expression patterns of Split GAL4 lines from Janelia Research Campus Janelia FlyLight Project Team
Gerry Rubin Lab
Janelia Research Campus
Virginia, USA
Fly Trap Database of classical P(GAL4) enhancer traps imaged in head sections Armstrong Lab
University of Edinburgh
Edinburgh, UK
DoOR Database of odorant responses in Drosophila Munch and Galizia, 2016
NeuroMorpho Curated inventory of digitally reconstructed neurons associated with peer-reviewed publications Ascoli et al., 2007
Insect Brain Database Database of single neurons and brains for several insect species Uwe Homberg Lab
Randolf Menzel Lab
Marie Dacke/Basil el Jundi Labs
Bente Berg Lab
Stanley Heinze Lab


For viewing, analysing and querying images

Resource Description Author/Source
Virtual Fly Brain Interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster Milyaev et al., 2012
Bridging registrations This site provides the tools to transform image data from one template brain (adult Drosophila) to another, using a bridging registration. Manton et al., 2014
NBLAST Tool to search for similar neurons by morphology and location Costa et al., 2014


Interactive maps

Resource Description Author/Source
Embryonic and larval neuroblasts and lineages Interactive maps of the embryonic and larval neuroblasts and lineages Christof Rickert
University of Mainz
Mainz, Germany
FlyPNS Description of embryonic and larval sensory organs of D. melanogaster in abdominal segments A1-A7 Orgogozo and Grueber, 2005


Nomenclature and protocols

Resource Description Author/Source
BrainName Standard nomenclature of the adult brain Ito et al., 2014
Immunostaining of adult brains This protocol describes the dissection, staining, and imaging of adult brains from Drosophila with mosaic labeling Ostrovsky et al., 2013
Image registration of adult brains This protocol describes the practical steps required for an intensity-based nonlinear registration of the Drosophila brain using the staining for the presynaptic marker Bruchpilot (nc82) Ostrovsky et al., 2013


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