Difference between revisions of "FlyBase:Images"

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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;"| [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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| [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</br> University of Edinburgh<br/>Edinburgh, UK
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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<br/> University of Edinburgh<br/>Edinburgh, UK
 
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|style="background: #efefef;"| [http://www.fly-trap.org/ Flytrap brain] ||style="background: #efefef;"| Vintage 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;"| [http://www.fly-trap.org/ Flytrap brain] ||style="background: #efefef;"| Vintage 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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| [http://cooley.medicine.yale.edu/flytrap/ Flytrap ovary - retired] ||Deprecated database of Flytraps imaged in ovaries.||Cooley Lab</br> Yale School of Medicine</br> New Haven, CT, USA
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| [http://cooley.medicine.yale.edu/flytrap/ Flytrap ovary - retired] ||Deprecated database of Flytraps imaged in ovaries.||Cooley Lab<br/> Yale School of Medicine<br/> New Haven, CT, USA
 
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= CRISPR Stocks =
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= Tools for General Image Analysis =
  
 
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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;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef;"| The Bloomington Stock Center's CRISPR/Cas9 page. Includes stocks for expression of both Cas9 nuclease and tracrRNA. ||style="background: #efefef;"| Bloomington Drosophila Stock Center (BDSC)<br/> Indiana University<br/> Bloomington, IN, USA
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|style="white-space: nowrap; background: #efefef;"| [http://fiji.sc ImageJ/Fiji]||style="background: #efefef;"| Widely used open source platform for research in biological image analysis. Many plugins were developed around ''Drosophila'' centric projects. ||style="background: #efefef;"| Eliceiri Lab<br/> University of Wisconsin-Madison<br/>Madison, WI, USA<br/>Tomancak lab<br/> Max Planck Institute of Molecular Cell Biology and Genetics<br/>Dresden, Germany
 
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| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || Detailed information on stocks generated by the CRISPR Fly Design group at the MRC Laboratory of Molecular Biology (available from [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm the BDSC]).  ||style="white-space: nowrap;"| MRC Laboratory of Molecular Biology<br /> Cambridge, UK
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| [http://home.penglab.com/proj/vaa3d/home/index.html Vaa3D] || A platform aspiring to be a "Swiss army knife for big image data". Originally developed at Janelia Research Campus around ''Drosophila'' neurobiology projects.||style="white-space: nowrap;"| Peng Lab<br/> Allen Institute<br/> Washington, USA
 
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|style="background: #efefef;"| [http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG-FLY CRISPR/Cas9] ||style="background: #efefef;"| Reagents, protocols, and online tools developed for genome engineering in <em>Drosophila</em>. ||style="background: #efefef;"| NIG-FLY<br/> National Institute of Genetics<br/> Mishima, Japan
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|style="background: #efefef;"| [http://ilastik.org/ Ilastik] ||style="background: #efefef;"| 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.||style="background: #efefef;"| NIG-FLY<br/> National Institute of Genetics<br/>Olivo-Marin Lab<br/>Institut Pasteur<br/>Paris, France
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| [http://icy.bioimageanalysis.org/ Icy] || Generalist open source image analysis platform with diverse functions. Not specifically connected to ''Drosophila'' research.||style="white-space: nowrap;"| Quantitative Image Analysis Unit<br/>Institut Pasteur<br/>Paris, France
 
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Revision as of 19:18, 8 August 2015

Popular Resource Categories

All Resources CRISPR RNAi Stocks Antibodies Images

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

Imaged 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
A database of Drosophila embryo and larvae mRNA localization patterns 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
Expression Patterns of GAL4 and LexA Driver Lines 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
Flytrap brain Vintage database of classical P(GAL4) enhancer traps imaged in head sections. Armstrong Lab
University of Edinburgh
Edinburgh, UK
Flytrap ovary - retired Deprecated database of Flytraps imaged in ovaries. Cooley Lab
Yale School of Medicine
New Haven, CT, 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


CRISPR Vectors

Resource Description Author/Source
Addgene CRISPR/Cas9 Plasmids for use in insects A list of available Cas9 & gRNA expression plasmids for use in insects, including Drosophila. Addgene
Cambridge, MA, USA
CRISPR Fly Design Plasmids Descriptions and information regarding the plasmids created by the CRISPR Fly Design group (also deposited at Addgene). MRC Laboratory of Molecular Biology
Cambridge, UK
NIG-FLY CRISPR/Cas9 Reagents, protocols, and online tools developed for genome engineering in Drosophila. NIG-FLY
National Institute of Genetics
Mishima, Japan


Additional Useful CRISPR Links

Resource Description Author/Source
CRISPR Fly Design Reagents, protocols, and results from fly CRISPR/Cas9 experiments. MRC Laboratory of Molecular Biology
Cambridge, UK
flyCRISPR An overview and resource collection for CRISPR gene editing in Drosophila. O'Connor-Giles, Wildonger, and Harrison Labs
University of Wisconsin-Madison
WI, USA
Insect Genomic Technologies Research Coordination Network Discussion and dissemination of advanced technologies for genome modification of insects through symposia, technical workshops, and training fellowships. Institute for Bioscience and Biotechnology Research
University of Maryland
Rockville, MD, USA
FlyRNAi Blog, CRISPR tags A research blog tracking functional genomics techniques in Drosophila, filtered for keyword: CRISPRs. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
DRSC Single Cell Cloning Protocol Single-cell cloning method useful for Drosophila cell CRISPR gene editing. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
OXfCRISPR Information about protocols and reagents, new refinements of techniques, useful links to other tools, websites, and discussion groups. Liu lab
University of Oxford
Oxford, UK


Selected recent CRISPR method reviews

Selected recent CRISPR method reports for tissue culture cells

Selected recent CRISPR method reports for in vivo


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