Difference between revisions of "FlyBase:Images"
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| − | =Popular Resource Categories= | + | = Popular Resource Categories = |
{|class="wikitable" | {|class="wikitable" | ||
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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: 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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| + | {|class="wikitable" | ||
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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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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. | 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. | ||
| − | = | + | = Image Based Resources = |
{|cellpadding=5 | {|cellpadding=5 | ||
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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/ | + | | [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 |
|- | |- | ||
|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 | ||
|- | |- | ||
| − | | [ | + | | [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 |
|- | |- | ||
|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;"| [ | + | |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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| − | | [ | + | | [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;"| [ | + | |style="background: #efefef;"| [https://figshare.com/projects/An_anatomical_atlas_of_Drosophila_melanogaster_-_the_wildtype/218623 SEM (scanning electron microscope) Drosophila anatomy atlas] ||style="background: #efefef;"| A collection of labelled scanning electron microscope images comprising many prominent anatomical details of D. melanogaster larvae, pupae, and adults.||style="background: #efefef;"| Paululat Lab<br/> Osnabrück University<br/> Osnabrück, Germany |
|- | |- | ||
| − | | [http:// | + | | [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 |
|- | |- | ||
| + | |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://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 | | [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 | ||
|- | |- | ||
| − | |style="background: #efefef;"| [http://ilastik.org/ | + | |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 |
|- | |- | ||
| [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 | | [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 | ||
Latest revision as of 18:50, 5 November 2024
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 |
| OpenOrganelle | Open access electron microscopy atlas. Explore cells and tissue at nanometer resolution. Drosophila brain images. | Janelia Research Campus Ashburn, VA, USA |
| SEM (scanning electron microscope) Drosophila anatomy atlas | A collection of labelled scanning electron microscope images comprising many prominent anatomical details of D. melanogaster larvae, pupae, and adults. | Paululat Lab Osnabrück University Osnabrück, Germany |
| 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 |
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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