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Biomedicum Imaging Unit

Faculty of Medicine



Biomedicum Imaging Unit (BIU)



Biocenter Finland



Contact information


5th floor office, room B501a
Tel: +358 2941 25269

1st floor office, room B117a
Tel: +358 2941 25271

Biomedicum Helsinki
PO Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki


Microscopy and Imaging
(commercial reference sites)

Microscopy and Imaging
(non-commercial reference sites)

Microscopy and imaging networks

Fluorophores and other molecular/cell biology products

Fluorophore properties

Free imaging software

Commercial imaging software

Other imaging facilities


Microscopy and Imaging (commercial reference sites)    


Optical filters - check also their resources that contain useful information about filters in general (handbook and application notes), and fluorescent protein filters (GFP catalog and application notes)


CCD cameras, light sources, lasers, fibre optics etc.


Special microscopy slides

Leica Microsysytems

Short descriptions on Leica's products


Glass bottom culture dishes for live cell imaging

Nikon Instruments

About Nikon microscopes. On the web page, click on the  Microscopy techniques button to find a nice visual presentation on microscopy.

Nikon has also an outstanding web site that offers a weath of information on  confocal microscopy, as well as on wide-field microscopy. Learn about sample preparation, aberrations, and other important aspects of confocal imaging. Based on Molecular Expressions.

Nikon's Small World photomicrography competition is open for everyone.

Olympus Biosystems

Info on Olympus microscopes. Olympus has excellent web pages on confocal microscopy, full of useful information on fluorophores, spectral bleed-through, resolution and contrast, objectives etc. Highly recommended. Based on Molecular Expressions


Optical filters - Curv-o-matic is an excellect tool: An interactive database of fluorophore absorption and emission spectra, along with filter set recommendations and accompanying filter spectral curves

Perkin-Elmer In Vivo Imaing

In vivo imaging systems for whole mice and rats (bioluminescence or fluorescence)

Thermo Scientific

High content Screening and Analysis.

Zeiss Microscopy web page

Information on Zeiss products.

Microscopy and Imaging (non-commercial reference sites)    

iBiology Microscopy Course

An online course covering all aspects of light microscopy in a series of video lectures. There is also a short course covering the basics.

Molecular Expressions

Excellent microscopy reference for beginners and experts by M. W. Davidson and the Florida State Universisty

NINDS Gensat

NINDS GENSAT BAC Transgenics Project (The Rockefeller University): The Gensat database contains a gene expression atlas of the central nervous system of the mouse based on bacterial artificial chromosomes (BACs). In each of the BAC transgenic vectors, endogenous protein coding sequences have been replaced by sequences encoding the EGFP reporter gene

Microscopy and imaging networks
Euro-BioImaging Euro-BioImaging is a pan-European infrastructure project whose mission is to build a distributed imaging infrastructure across Europe that will provide open access to innovative biological and medical imaging technologies for European researchers.

ELMI (European Light Microscopy Initiative)

ELMI is a communication network between European scientists working in the field of light microscopy and the manufacturers. BIU is a member of ELMI.

Fluorophores and other molecular/cell biology products     
Antibodies-online An antibodies marketplace


Novel Fluorescent Proteins etc. Part of Takara Bio.


CSHL Press provided web site where you can search  for scientific supplies

Cell Signaling

Primary antibodies for signal transduction molecules

eBioscience Offering eFluor organic dyes and nanocrystals


Photoactivable fluorescent proteins etc.

Fluorescent protein properties

A plotting tool for different protein properties.

Thermo Fisher Scientific


Jackson ImmunoResearch Europe

Labeled secondary antibodies etc.

MBL International

Sells CoralHue fluorescent proteins, also photochromic ones that are turned on or off on demand by exposure to different wavelenghts of light.

Molecular Probes

Subdivision of Invitrogen. Large selection of fluorescent probes. The excellent Molecular Probes Handbook is available online. Includes Fluorescence Spectra Viewer (if you visit the page for the first time, you first have to select Finland, then continue, to get to the Viewer).

Sigma-Aldrich's RNAi Consortium shRNA library

Lentiviral-based shRNA vectors for transient or stable transfection, as well as viral particle generation. The complete libraries will target 15000 human and 15000 mouse genes.

Antibodies as well as other immunohistochemistry /immunofluorescence products

Fluorophore properties

Fluorescent protein properties

A plotting tool for different fluorescent protein properties.

Fluorescence Spectra Viewer (ThermoFisher)

A tool for plotting spectral overlap and excitation efficiences of fluorescent labels.

Fluorescence Spectra Viewer (Chroma)

A tool for plotting spectral overlap and excitation efficiences of fluorescent labels.

Free imaging software     


Free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images. First beta version available.


CellProfiler is a free open source software designed to quantitatively measure phenotypes from thousands of images automatically.


Fiji is an image processing package. It can be described as a "batteries-included" distribution of ImageJ (and ImageJ2).


Icy provides the software resources to visualize, annotate and quantify bioimaging data.


NIH program for image processing and analysis. (Windows, Mac OS 9, Mac OS X, Linux)

ImageJ mailing list

Discussion list for ImageJ users and developers. Also list archives.


ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats


ImageJ plugin that corrects x-y movement of images in time-lapse image stacks

Kyoto Encyclopedia of Genes and Genomes

KEGG is a 2-D visualization tool for metabolic pathways


Scientific data visualizer


An open source software for image acquisition. ImageJ compatible user interface. Matlab programs can be utilized in Micro-Manager. (Windows, Mac, Linux).


Medical Image Processing, Analysis, and Visualization; NIH Java application that enables quantitative analysis and visualization of PET, MRI, CT, and microscopy images

Open Microscopy Environment

OME is an open source software project to develop a database-driven system for the quantitative analysis of biological images


An ImageJ plugin for the automatic alignment of a source image or a stack to a target image

Virtual Cell

Virtual Cell software from the National Resource for Cell Analysis and Modeling allows simulation of e.g. FRAP data and membrane diffusion.


VioBIo is designed for visualization and analysis of multidimensional image data (Windows, Mac, Linux)


ImageJ plugin for volume rendering by Michael D. Abramoff.


Voxel-based real-time 3D image processing and rendering of multi-channel 3D and 4D data. (Windows, Mac OS X, Linux)

Commercial imaging software     


Imaris multidimensional image data rendering, visualization, and analysis software.

Leica LAS X

Leica LAS X software. Lite version available for Windows 7.


Nikon imaging software. NIS-Elements Viewer available for Windows and OS X.

Scientific Volume Imaging

Huygens deconvolution software, also FluVR volume rendering software


Zeiss imaging software (Zen, AxioVision, and LSM Image Browser)

Other imaging facilities     

Light Microscopy Unit

Institute of Biotechnology (Viikki Campus)

Cell Imaging Core

Turku Centre for Biotechnology

Advanced Microscopy Unit Electron, confocal and DIC microscopy. At Haartman institute (HFIC, BCIC)
Helsinki Functional Imaging Center Coordinates the imaging activities in the Helsinki area

Page updated 24.10.2016

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