FlyBase:Images
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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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