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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
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
Brain Trap	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.	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

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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