Advance Imaging Facility

Guidelines for Best Practices for image processing.

Online microscope courses:

YouTube microcourses
iBiology microscopy series
Myscope microscopy training

Free Online Image Databases:

See also the EuroBioImaging Fairsharing page.

- Cell Centered Database: "This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes".
- Cell Image library: a repository of images and movies of cells from a variety of organisms. Looks good.
- CYCLoPS Collection of Yeast Cells and Localization PaternS. Chong et al. (2015) Cell 161: 1413-1424.
- Genome-wide database of mitosis, RNA interference screens to identify all proteins that are required for mitosis in human cells. Neamann et al. (2010) Nature 464: 721-727.
- GFP Arabidposis database, John Innes Institute, UK. Related article: Koroleva et al. (2005) Plant J 41: 162-174.
- Image Data Resource (IDR) "The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies,
where the community can submit, search and access high-quality bio-image data.". Williams et al. (2016).
- NeuroData: A community-developed open-source computational ecosystem for big neuro data. week. Vogelstein et al. (2018).
- Systems Science of Biological Dynamics (SSBD) store and share quantitative data of spatiotemporal dynamics of biological objects. Tohsato et al. (2016).
- The American Society for Cell Biology's Image and Video library: a collection of images, videos, and digital texts that illustrate the structure, function and biology of the cell.
- The human protein atlas: "contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data".
- The Kahn Dynamic Proteomics Database, Weizmann Institute of Science, Israel. Each human cell-line clone contains an endogenous protein fused to YFP. Related article: Frankel-Morgenstern et al (2009) Nucl Acid Res 1-5.
- The Mouse Connectome Project, this project aims to create a three-dimensional digital connectome atlas of the C57Black/6J mouse brain. Zinng et al. (2014) Cell 156: 1096–1111.- VisiGene Image Browser: VisiGene is a virtual microscope for viewing in situ images from mouse and Xenopus.
- Yeast-GFP: Yeast GFP Fusion Localization Database.
- Yeast Protein Localization Database: Subcellular localization of proteins in the yeast Saccharomyces cerevisiae.

Fluorescence excitation and emission spectra:

- - The database of fluorescent dyes and applications (University of Graz).
- Spectral viewer from university of Arizona (includes 2P excitation data).
- Spectra Viewer Thermo Fisher Scientific.
- BD Fluorescence Spectrum Viewer.
- Overview of fluorescent protein properties; Nikon Imaging Centre UCSF.
- SearchLight from Semrock.

Links to microscope resources:

- UK Light Microscopy Facilities A list of facilities and microscope systems in the UK.
- Nature Mile Stones in Light Microscopy
- Leica Science Lab
- Molecular Expressions website
Molecular Probes® School of Fluorescence
- Nikon Microscopy U
- Olympus Microscopy Resource Center
- Zeiss online campus


Benchmark and test datasets

- Broad Bioimage Benchmark Collection
- Colocalization Benchmark Source.
- Data sets for automatic segmentation of neural structures in ssTEM
- EPFL reference datasets for single molecule localization microscopy
- OME sample images
- OpenSlide project test data
TUT Benchmark of simulated cell images
- UCSB Bio-Segmentation Benchmark dataset.

Links to technical websites:

- Microscope Station: overview of microscopes, techniques, reagents etc.
- Portal for Immunohistochemistry & In Situ Hybridization: Protocols, antibody search etc.
- Protocol Online: Image Techniques.
- Light Microscopy Research Group: stadarisation in optical microscopy

Check also the Tips and Tricks webpage

The microscope facilities would not be possible without the help and support from the following companies (alphabetically):



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