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: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>
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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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__TOC__  
 
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This image-based resources page has been generously contributed by [https://www.mpi-cbg.de/research-groups/current-groups/pavel-tomancak/research-focus/ Pavel Tomancak] of the Max Planck Institute of Molecular Cell Biology and Genetics.
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This image-based resources page has been generously contributed by [https://www.mpi-cbg.de/research-groups/current-groups/pavel-tomancak/research-focus/ '''Pavel Tomancak'''] of the Max Planck Institute of Molecular Cell Biology and Genetics.
  
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= Imaged Based Resources =
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= Image Based Resources =
  
 
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|style="white-space: nowrap; background: #efefef;"| [http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Patterns of gene expression in ''Drosophila'' embryogenesis] ||style="background: #efefef;"| Database of 2D images and annotations of patterns of gene expression during ''Drosophila'' embryogenesis revealed by RNA ''in situ'' hybridisation.||style="white-space: nowrap; background: #efefef;"|Berkeley Drosophila Genome Project (BDGP)<br/> Lawrence Berkeley National Laboratory<br/>Berkeley, CA, USA
 
|style="white-space: nowrap; background: #efefef;"| [http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Patterns of gene expression in ''Drosophila'' embryogenesis] ||style="background: #efefef;"| Database of 2D images and annotations of patterns of gene expression during ''Drosophila'' embryogenesis revealed by RNA ''in situ'' hybridisation.||style="white-space: nowrap; background: #efefef;"|Berkeley Drosophila Genome Project (BDGP)<br/> Lawrence Berkeley National Laboratory<br/>Berkeley, CA, USA
 
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| [http://fly-fish.ccbr.utoronto.ca/ 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<br/> University of Toronto<br/> Toronto, Ontario, Canada
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| [http://fly-fish.ccbr.utoronto.ca/ 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<br/> University of Toronto<br/> Toronto, Ontario, Canada
 
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|style="background: #efefef;"|[http://www.flyrnai.org/crispr2/ DRSC Find CRISPR Tool] ||style="background: #efefef;"| A tool for discovering gRNA targets located throughout the fly genome (release 5). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets.  ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
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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
 
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| [http://cas9.cbi.pku.edu.cn/ Cas9 Design] || A CRISPR/Cas9 guide RNA design tool. Support for multiple species including fly (release 5), zebrafish, mouse, human, and others. || Center for Bioinformatics<br/> Peking University<br/> Beijing, China
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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://crispr.cos.uni-heidelberg.de/ CCTop] ||style="background: #efefef;"| CRISPR/Cas9 Target online predictor. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. Notably large set of configurable parameters. ||style="background: #efefef;"| Center for Organismal Studies<br/> University of Heidelberg<br/>Heidelberg, Germany
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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
 
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| [http://www.e-crisp.org/E-CRISP/designcrispr.html E-CRISP] || gRNA genome-wide target finder, searchable via  gene symbol or sequence. Relaxed, "medium", or strict search options. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. ||Boutros lab, DKFZ<br/> Heidelberg, Germany
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| [http://insitu.fruitfly.org/cgi-bin/ex/search.pl?ftype=6&ftext=_* 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)<br/> Lawrence Berkeley National Laboratory<br/>Berkeley, CA, USA
 
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|style="background: #efefef;"| [https://chopchop.rc.fas.harvard.edu/ CHOPCHOP] ||style="background: #efefef;"| Search for gRNA targets. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. Configurable options for off-targets, PAM motifs, and 5' requirements. ||style="background: #efefef;"| Schier & Church Labs<br /> Harvard University<br /> Cambridge, MA, USA
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|style="background: #efefef;"| [http://rablibrary.mpi-cbg.de/cgi-bin/rab_overview.pl FLYtRAB] ||style="background: #efefef;"| 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. ||style="background: #efefef;"|Eaton and Tomancak Labs<br/> Max Planck Institute of Molecular Cell Biology and Genetics<br/>Dresden, Germany
 
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| [http://crispr.mit.edu/ CRISPR Design] ||Identification of gRNA sites genome wide. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. || Zhang Lab<br /> MIT<br /> Boston, MA, USA
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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
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|style="background: #efefef;"| [http://tefor.net/crispor/crispor.cgi CRISPOR] ||style="background: #efefef;"| A program that helps design, evaluate, and clone guide sequences for the CRISPR/Cas9 system. Support for multiple species including several <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others.||style="background: #efefef;"| Tefor<br />France
 
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= CRISPR Stocks =
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
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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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|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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| [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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| [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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|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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|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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| [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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= CRISPR Vectors =
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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;"| [https://www.addgene.org/crispr/drosophila/ Addgene CRISPR/Cas9 Plasmids for use in insects]||style="white-space: nowrap; background: #efefef;"| A list of available Cas9 & gRNA expression plasmids for use in insects, including <em>Drosophila</em>. ||style="background: #efefef;"| Addgene<br />Cambridge, MA, 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/plasmids/ CRISPR Fly Design Plasmids] || Descriptions and information regarding the plasmids created by the CRISPR Fly Design group (also [http://www.addgene.org/search/advanced/?q=Bullock#p=true deposited at Addgene]). || 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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= Additional Useful CRISPR Links =
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= Tools for Image Visualization and Annotation =
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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://www.crisprflydesign.org/ CRISPR Fly Design]||style="white-space: nowrap; background: #efefef;"| Reagents, protocols, and results from fly CRISPR/Cas9 experiments. ||style="background: #efefef;"| MRC Laboratory of Molecular Biology<br /> Cambridge, UK
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|style="white-space: nowrap; background: #efefef;"| [http://catmaid.org CATMAID]||style="background: #efefef;"|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.||style="background: #efefef;"|Cardona Lab<br/> Janelia Research Campus<br/> Ashburn, VA, USA<br/>Tomancak lab<br/> Max Planck Institute of Molecular Cell Biology and Genetics<br/>Dresden, Germany
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| [http://flycrispr.molbio.wisc.edu/ flyCRISPR] || An overview and resource collection for CRISPR gene editing in <em>Drosophila</em>. || O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA
 
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| style="background: #efefef;"| [http://igtrcn.org/ Insect Genomic Technologies Research Coordination Network] || style="background: #efefef;"| Discussion and dissemination of advanced technologies for genome modification of insects through symposia, technical workshops, and training fellowships. || style="background: #efefef; white-space: nowrap;"|Institute for Bioscience and Biotechnology Research<br />University of Maryland<br />Rockville, MD, USA
 
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| [http://flyrnai.blogspot.com/search/label/CRISPRs FlyRNAi Blog, CRISPR tags] || A research blog tracking functional genomics techniques in <em>Drosophila</em>, filtered for keyword: CRISPRs. || Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
 
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|style="background: #efefef;"| [http://www.flyrnai.org/DRSC-Protocol_single_cell_cloning.html DRSC Single Cell Cloning Protocol] ||style="background: #efefef;"| Single-cell cloning method useful for <em>Drosophila</em> cell CRISPR gene editing. ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
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| [http://www.openmicroscopy.org/site/products/omero 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<br/> University of Dundee<br/> Dundee, UK
 
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|[http://www.dpag.ox.ac.uk/research/liu-group/liu-group-news/oxfcrispr OXfCRISPR] ||Information about protocols and reagents, new refinements of techniques, useful links to other tools, websites, and discussion groups. || Liu lab<br/> University of Oxford<br/> Oxford, UK
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|style="background: #efefef;"| [http://www.cytomine.be/ Cytomine] ||style="background: #efefef;"| An open-source rich internet application for collaborative analysis of multi-gigapixel images. Focusing on histology data. ||style="background: #efefef;"|Systems and Modeling group<br/>University of Liège<br/>Liège, Belgium
 
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= Selected recent CRISPR method reviews =
 
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*  Venken KJ, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. [http://www.ncbi.nlm.nih.gov/pubmed/26447401 '''Genome engineering: Drosophila melanogaster and beyond.'''] Wiley Interdiscip Rev Dev Biol. 2015 Oct 8. doi: 10.1002/wdev.214. [Epub ahead of print<nowiki>]</nowiki> Review. PubMed PMID: 26447401.
 
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* Gratz1 SJ, Rubinstein CD, Harrison MM, Wildonger J, O'Connor-Giles KM [http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb3102s111/full '''CRISPR-Cas9 Genome Editing in Drosophila'''] Curr Protoc Mol Biol. 2015 Jul 1;111:31.2.1-31.2.20. doi: 10.1002/0471142727.mb3102s111. PMID: 26131852; PMCID: PMC4506758.
 
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*  Beumer KJ, Carroll D. [http://www.ncbi.nlm.nih.gov/pubmed/24412316 '''Targeted genome engineering techniques in Drosophila.'''] Methods. 2014 Jun 15;68(1):29-37. doi: 10.1016/j.ymeth.2013.12.002. Epub 2014 Jan 8. Review. PubMed PMID: 24412316; PubMed Central PMCID: PMC4048800.
 
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*  Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/25953352 '''A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila. J Genet Genomics.'''] 2015 Apr 20;42(4):141-9. doi: 10.1016/j.jgg.2015.02.007. Epub 2015 Mar 12. Review. PubMed PMID: 25953352.
 
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= Selected recent CRISPR method reports for tissue culture cells =
 
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*  Bassett AR, Tibbit C, Ponting CP, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/24326186 '''Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9.'''] Biol Open. 2014 Jan 15;3(1):42-9. doi: 10.1242/bio.20137120. PMID: 24326186.
 
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*  Böttcher R, Hollmann M, Merk K, Nitschko V, Obermaier C, Philippou-Massier J, Wieland I, Gaul U, Förstemann K. [http://www.ncbi.nlm.nih.gov/pubmed/24748663 '''Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells.'''] Nucleic Acids Res. 2014 Jun;42(11):e89. doi: 10.1093/nar/gku289. Epub 2014 Apr 19. PMID: 24748663
 
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*  Bassett AR, Kong L, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/24748663 '''A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells.'''] J Genet Genomics. 2015 Jun 20;42(6):301-9. doi: 10.1016/j.jgg.2015.03.011. Epub 2015 Apr 18. PMID: 26165496
 
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* Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, Lin S, Buckner M, Tao R, Yilmazel B, Mohr SE, Manning BD, Perrimon N. [http://www.ncbi.nlm.nih.gov/pubmed/26350902 '''Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi.'''] Sci Signal. 2015 Sep 8;8(393):rs9. doi: 10.1126/scisignal.aab3729. PMID: 26350902
 
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= Selected recent CRISPR method reports for <em>in vivo</em> =
 
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* Gratz SJ, Cummings AM, Nguyen JN, Hamm DC, Donohue LK, Harrison MM, Wildonger J, O'Connor-Giles KM. [http://www.ncbi.nlm.nih.gov/pubmed/23709638 '''Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease.'''] Genetics. 2013 Aug;194(4):1029-35. doi: 10.1534/genetics.113.152710. Epub 2013 May 24. PMID: 23709638
 
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* Bassett AR, Tibbit C, Ponting CP, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/23827738 '''Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system.'''] Cell Rep. 2013 Jul 11;4(1):220-8. doi: 10.1016/j.celrep.2013.06.020. Epub 2013 Jul 1. PMID: 23827738
 
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* Yu Z, Ren M, Wang Z, Zhang B, Rong YS, Jiao R, Gao G. [http://www.ncbi.nlm.nih.gov/pubmed/23833182 '''Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila.'''] Genetics. 2013 Sep;195(1):289-91. doi: 10.1534/genetics.113.153825. Epub 2013 Jul 5. PMID: 23833182
 
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* Kondo S, Ueda R. [http://www.ncbi.nlm.nih.gov/pubmed/24002648 '''Highly improved gene targeting by germline-specific Cas9 expression in Drosophila.'''] Genetics. 2013 Nov;195(3):715-21. doi: 10.1534/genetics.113.156737. Epub 2013 Sep 3. PMID: 24002648
 
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* Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu LP, Yang Z, Mao D, Sun L, Wu Q, Ji JY, Xi J, Mohr SE, Xu J, Perrimon N, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/24191015 '''Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9.'''] Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19012-7. doi: 10.1073/pnas.1318481110. Epub 2013 Nov 4. PMID: 24191015
 
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* Port F, Muschalik N, Bullock SL. [http://www.ncbi.nlm.nih.gov/pubmed/25999583 '''Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research.'''] G3 (Bethesda). 2015 May 20;5(7):1493-502. doi: 10.1534/g3.115.019083. PMID: 25999583
 
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* Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/25437567 '''Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila.'''] Cell Rep. 2014 Nov 6;9(3):1151-62. doi: 10.1016/j.celrep.2014.09.044. Epub 2014 Oct 23. PMID: 25437567
 
 
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&nbsp; [[#top|Back to top.]] | [[FlyBase:External_Resources|Back to All Resources Page.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
 
&nbsp; [[#top|Back to top.]] | [[FlyBase:External_Resources|Back to All Resources Page.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
  
 
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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
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Databases		 Images Maps Protocols Papers with
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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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