Difference between revisions of "FlyBase:Images"

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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:Stocks|Stocks]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Model_Organism_Databases|Model Organism<br/> Databases]]</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:Neuroscience|Neuroscience]]</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:Maps|Maps]]</big> ||style="text-align: center; padding: 20px;"| <big>[http://www.flyrnai.org/tools/protocols/web/ Protocols]</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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|style="background: #efefef;"|[http://tomancak-srv1.mpi-cbg.de/DOT/main.html Dresden Ovary Table] ||style="background: #efefef;"|Database of 3D images and annotations of patterns of RNA localisation in ''Drosophila'' ovaries revealed by fluorescent RNA ''in situ'' hybridisation. ||style="background: #efefef;"| Tomancak lab<br/> Max Planck Institute of Molecular Cell Biology and Genetics<br/>Dresden, Germany
 
|style="background: #efefef;"|[http://tomancak-srv1.mpi-cbg.de/DOT/main.html Dresden Ovary Table] ||style="background: #efefef;"|Database of 3D images and annotations of patterns of RNA localisation in ''Drosophila'' ovaries revealed by fluorescent RNA ''in situ'' hybridisation. ||style="background: #efefef;"| Tomancak lab<br/> Max Planck Institute of Molecular Cell Biology and Genetics<br/>Dresden, Germany
 
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| [http://flweb.janelia.org/cgi-bin/flew.cgi FlyLight] || Database of images and annotation of patterns driven by systematically generated enhancer constructs (Rubin collection) in wing imaginal discs, larval nervous system and adult brain.|| Rubin, Truman, Doe, and Mann Labs<br/> Janelia Research Campus<br/> Ashburn, VA, USA
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| [https://www.janelia.org/project-team/flylight FlyLight] || Database of images and annotation of patterns driven by systematically generated enhancer constructs (Rubin collection) in wing imaginal discs, larval nervous system and adult brain.|| Rubin, Truman, Doe, and Mann Labs<br/> Janelia Research Campus<br/> Ashburn, VA, USA
 
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|style="background: #efefef;"| [http://enhancers.starklab.org/ Fly Enhancers] ||style="background: #efefef;"| Database of 2D images and annotation of patterns driven by systematically generated enhancer constructs (Dickson collection) in embryos.||style="background: #efefef;"| Stark Lab<br/> Research Institute of Molecular Pathology<br/>Vienna, Austria
 
|style="background: #efefef;"| [http://enhancers.starklab.org/ Fly Enhancers] ||style="background: #efefef;"| Database of 2D images and annotation of patterns driven by systematically generated enhancer constructs (Dickson collection) in embryos.||style="background: #efefef;"| Stark Lab<br/> Research Institute of Molecular Pathology<br/>Vienna, Austria
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| [http://www.flyprot.org/ The FLAnnotator] ||Database of images and annotations of Cambridge protein trap lines.||St Johnston Lab<br/>Wellcome Trust/Cancer Research UK Gurdon Institute<br/>Cambridge, UK
 
| [http://www.flyprot.org/ The FLAnnotator] ||Database of images and annotations of Cambridge protein trap lines.||St Johnston Lab<br/>Wellcome Trust/Cancer Research UK Gurdon Institute<br/>Cambridge, UK
 
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|style="background: #efefef;"| [http://flypush.imgen.bcm.tmc.edu/pscreen/rmce/ MiMIC RMCE lines] ||style="background: #efefef;"| Database of images of MiMIC lines in larval CNS (GFP staining).||style="background: #efefef;"| Bellen Lab<br/> Baylor College of Medicine <br/>Houston, TX, USA
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|style="background: #efefef;"| [https://flypush.research.bcm.edu/pscreen/mimic.html MiMIC RMCE lines] ||style="background: #efefef;"| Database of images of MiMIC lines in larval CNS (GFP staining).||style="background: #efefef;"| Bellen Lab<br/> Baylor College of Medicine <br/>Houston, TX, USA
 
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| [http://www.virtualflybrain.org/site/vfb_site/home.htm Virtual Fly Brain] ||Sophisticated hub of Drosophila neuroanatomy data including several large sets of 3D scans of neuronal enhancer traps mapped onto a 3D atlas. ||Armstrong Lab, University of Edinburgh, Edinburgh, UK<br/> Greg Jefferis, MRC-LMB, Cambridge, UK<br/>O'Kane lab, University of Cambridge, Cambridge, UK<br/>Parkinson group, EMBL-EBI, Hinxton, UK
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| [http://www.virtualflybrain.org/ Virtual Fly Brain] ||Sophisticated hub of Drosophila neuroanatomy data including several large sets of 3D scans of neuronal enhancer traps mapped onto a 3D atlas. ||Armstrong Lab, University of Edinburgh, Edinburgh, UK<br/> Greg Jefferis, MRC-LMB, Cambridge, UK<br/>O'Kane lab, University of Cambridge, Cambridge, UK<br/>Parkinson group, EMBL-EBI, Hinxton, UK
 
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|style="background: #efefef;"| [http://fruitfly.inf.ed.ac.uk/braintrap/ Brain Trap] ||style="background: #efefef;"| Database of 3D confocal datasets showing reporter gene expression and protein localization in the adult Drosophila brain. Full size images throughout the volume of the entire brain are viewed interactively.||style="background: #efefef;"| St. Johnston Lab, University of Cambridge, Cambridge, UK<br/> Russell Lab, University of Cambridge, Cambridge, UK
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|style="background: #efefef;"| [http://cooley.medicine.yale.edu/flytrap/ FlyTrap Ovary - retired] ||style="background: #efefef;"| Deprecated database of Flytraps imaged in ovaries.||style="background: #efefef;"| Cooley Lab<br/> Yale School of Medicine<br/> New Haven, CT, USA
 
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| [http://www.fly-trap.org/ FlyTrap Brain] ||Vintage database of classical P(GAL4) enhancer traps imaged in head sections.||Armstrong Lab<br/> University of Edinburgh<br/>Edinburgh, UK
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| [https://openorganelle.janelia.org/ OpenOrganelle] ||Open access electron microscopy atlas. Explore cells and tissue at nanometer resolution. Drosophila brain images. ||<br/> Janelia Research Campus<br/> Ashburn, VA, USA
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|style="background: #efefef;"| [http://cooley.medicine.yale.edu/flytrap/ FlyTrap Ovary - retired] ||style="background: #efefef;"| Deprecated database of Flytraps imaged in ovaries.||style="background: #efefef;"| Cooley Lab<br/> Yale School of Medicine<br/> New Haven, CT, USA
 
 
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Latest revision as of 21:20, 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

This image-based resources page has been generously contributed by Pavel Tomancak of the Max Planck Institute of Molecular Cell Biology and Genetics.

Image Based Resources

Resource Description Author/Source
Patterns of gene expression in Drosophila embryogenesis Database of 2D images and annotations of patterns of gene expression during Drosophila embryogenesis revealed by RNA in situ hybridisation. Berkeley Drosophila Genome Project (BDGP)
Lawrence Berkeley National Laboratory
Berkeley, CA, USA
Fly-FISH Database of 2D images and annotations of patterns of gene expression and RNA localisation in Drosophila embryos and larval tissues revealed by fluorescent RNA in situ hybridisation. Krause Lab
University of Toronto
Toronto, Ontario, Canada
Dresden Ovary Table Database of 3D images and annotations of patterns of RNA localisation in Drosophila ovaries revealed by fluorescent RNA in situ hybridisation. Tomancak lab
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
FlyLight Database of images and annotation of patterns driven by systematically generated enhancer constructs (Rubin collection) in wing imaginal discs, larval nervous system and adult brain. Rubin, Truman, Doe, and Mann Labs
Janelia Research Campus
Ashburn, VA, USA
Fly Enhancers Database of 2D images and annotation of patterns driven by systematically generated enhancer constructs (Dickson collection) in embryos. Stark Lab
Research Institute of Molecular Pathology
Vienna, Austria
CRMs at BDGP Database of images and annotation of patterns driven by systematically generated enhancer constructs (Rubin collection) in embryos. Berkeley Drosophila Genome Project (BDGP)
Lawrence Berkeley National Laboratory
Berkeley, CA, USA
FLYtRAB Expression of 27 (all) endogenously tagged rab proteins in salivary glands, larval brain, wing discs, ovaries, testis and fat body imaged by high resolution confocal microscopy. Visualised in CATMAID. Eaton and Tomancak Labs
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
The FLAnnotator Database of images and annotations of Cambridge protein trap lines. St Johnston Lab
Wellcome Trust/Cancer Research UK Gurdon Institute
Cambridge, UK
MiMIC RMCE lines Database of images of MiMIC lines in larval CNS (GFP staining). Bellen Lab
Baylor College of Medicine
Houston, TX, USA
Virtual Fly Brain Sophisticated hub of Drosophila neuroanatomy data including several large sets of 3D scans of neuronal enhancer traps mapped onto a 3D atlas. Armstrong Lab, University of Edinburgh, Edinburgh, UK
Greg Jefferis, MRC-LMB, Cambridge, UK
O'Kane lab, University of Cambridge, Cambridge, UK
Parkinson group, EMBL-EBI, Hinxton, UK
FlyTrap Ovary - retired Deprecated database of Flytraps imaged in ovaries. Cooley Lab
Yale School of Medicine
New Haven, CT, USA
OpenOrganelle Open access electron microscopy atlas. Explore cells and tissue at nanometer resolution. Drosophila brain images.
Janelia Research Campus
Ashburn, VA, USA


Tools for General Image Analysis

Resource Description Author/Source
ImageJ/Fiji Widely used open source platform for research in biological image analysis. Many plugins were developed around Drosophila centric projects. Eliceiri Lab
University of Wisconsin-Madison
Madison, WI, USA
Tomancak lab
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
Vaa3D A platform aspiring to be a "Swiss army knife for big image data". Originally developed at Janelia Research Campus around Drosophila neurobiology projects. Peng Lab
Allen Institute
Washington, USA
ilastik Simple, user-friendly tool for interactive image classification, segmentation and analysis. Brings the power of machine learning to biologists working with light and electron microscopy data. Build around Drosophila centric projects. NIG-FLY
National Institute of Genetics
Olivo-Marin Lab
Institut Pasteur
Paris, France
Icy Generalist open source image analysis platform with diverse functions. Not specifically connected to Drosophila research. Quantitative Image Analysis Unit
Institut Pasteur
Paris, France


Tools for Image Visualization and Annotation

Resource Description Author/Source
CATMAID Collaborative Annotation Toolkit for Massive Amounts of Image Data. Enables collaborative tracing of neurons in serial section electron microscopy data and visualisation, sharing and collaborative annotation of imaging-based screens. Very Drosophila centric. Cardona Lab
Janelia Research Campus
Ashburn, VA, USA
Tomancak lab
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
OMERO OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Very general, well supported tool. Swedlow Lab
University of Dundee
Dundee, UK
Cytomine An open-source rich internet application for collaborative analysis of multi-gigapixel images. Focusing on histology data. Systems and Modeling group
University of Liège
Liège, Belgium


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