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Interesting imaging articles in 2008
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| Jékely, G. and Arendt, D. Confocal Detection of NBT/BCIP In Situ Hybridization. Bionity articles, originally published in Biochemica 4/2007, p. 12-14. (This article describes how confocal microscope can be used for detection of NBT/BCIP signal in whole-mount in situ hybridization specimen). |
| Huang, B., Wang, W., Bates, M. and Zhuang, X. Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy. Scienceexpress Jan. 3 (2008). (STORM applied to 3D, reducing the lateral resolution to 20-30 nm, axial resolution to 50-60 nm). |
Bullen, A. Microscopic imaging techniques for drug discovery. Nature Rev. Drug Disc. 7, 54-67 (2008). (Illustrative review of latest light microscopy imaging techniques).June 21, 2010 |
Interesting imaging articles in 2007
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Shcherbo, D., Merzlyak, E. M., Chepurnykh, T. V., Fradkov, A. F., Ermakova, G. V.,
Solovieva, E. A., Lukyanov, K. A., Bogdanova, E. A., Zaraisky, A. G., Lukyanov, S. and
Chudakov, D. M. Bright far-red fluorescent protein for whole-body imaging. Nat. Methods 4, 741-746 (2007). (Katushka and its monomeric form mKate are novel bright far-red fluorescent proteins). |
| Lessard, G. A., Goodwin, P. M. and Werner, J. H. Three-dimensional tracking of individual quantum dots. Appl. Phys. Lett. 91 , 224106-109 (2007). (in vivo tracking of single molecules is made possible by using optical fibers couples to individual detectors). |
| Livet, J., Weissman, T. A., Kang, H., Draft, R. W., Lu, J., Bennis, R. A., Sanes, J. R., and Lichtman, J. W. Transgenic strategies for combinatorial expression. Nature 450, 56-62 (2007). (Visualization of neurons by genetically randomized expression of fluorescent proteins in Brainbow mice). |
| Chung, E., Kim, D., Cui, Y., Kim, Y.-H.and So, P. T. C.Two-Dimensional Standing Wave Total Internal Reflection Fluorescence Microscopy: Superresolution Imaging of Single Molecular and Biological Specimens. Biophys. J. 93, 1747-1757(2007). (Standing wave TIRF improves the resolution and signal/background ration of TIRF). |
Kremers, G.-J., Goedhart, J., van den Heuvel, D. J., Gerritsen, H. C. and
Gadella, Jr., T. W. J. Improved Green and Blue Fluorescent Proteins for Expression in Bacteria and Mammalian Cells. Biochemistry 46, 3775-3783. (2007). (The authors describe SGFP2 (strongly enhanced green fluorescent protein) and SBFP2 (strongly enhanced blue fluorescent protein) that are improved versions of EGFP and EBFP). |
| Pearson, H. The good, the bad and the ugly. Nature 447, 138-140 (2007). (Nature reporter discusses quality problems in published microscopy images in News Feature). |
| Kasthur, N. and Lichtman, J. W. The rise of the 'projectome'. Nature Meth 4, 307 - 308 (2007). (News and Views review of the next two papers listed below). |
| Verveer, P. J., Swoger, J., Pampaloni, F., Greger, K., Marcello, M and Stelzer, E. H. K. High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy. Nature Meth 4, 311 - 313 (2007). ( Combination of selective plane illumination microscopy (SPIM) and a new deconvolution algorithm allows imaging of large samples at high resolution with little photodamage). |
| Dodt, H.-U, Leischner, U., Schierloh, A., Jährling, N., Mauch, C. P., Deininger, K., Deussing, J. M., Eder, M., Zieglgänsberge, M. and Becker, K. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nature Meth 4, 331 - 336 (2007). (The authors describe a method of imaging the whole mouse brain with cellular resolution). |
| Bode, M. and Krusche, A. Toponome Imaging System (TIS): imaging the proteome with functional resolution. Nature Meth. 4 , iii-iv (2007). (An advertising feature on an automated fluorescent microscope that can image over 100 different proteins in a single cell or tissue section). |
| Donnert, D., Eggeling, C. and Hell, S. W. Major signal increase in fluorescence microscopy through dark-state relaxation. Nature Meth. 4, 81-86 (2007). (Pulsed, low-frequency excitation allows dark or triplet state relaxation, leading to reduced photobleaching and stronger signal). |
| Lamprecht, M., Sabatini, D. and Carpenter, A. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques 42, 71-75. (2007). (The authors describe their free, open-source high-throughput cell image analysis software). |
| Braeckmans, K., Remaut, K., Vandenbroucke, R., Lucas, B., De Smedt, S. and Demeeste, J. Line FRAP with the Confocal Laser Scanning Microscope for Diffusion Measurements in Small Regions of 3-D Samples. Biophys. J. 92, 2172-2183 (2007). (By using line scanning, the authors present a FRAP model that they claim is truly quantitative and easy to apply). |
| Hoebe, R., Van Oven, C., Gadella Jr, T., Dhonukshe, P., Van Noorden, C. and Manders, E. Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging . Nature Biotechnology 25, 249-253 (2007). (By controlling illumination according to the signal integrated from each pixel, the authors show significant reduction of photobleaching and phototoxicity in fluorescence confocal imaging of live cells). |
| Yudushkin, A., Schleifenbaum, A., Kinkhabwala, A., Neel, B., Schultz, C. and Bastiaens, P. Live-Cell Imaging of Enzyme-Substrate Interaction Reveals Spatial Regulation of PTP1B. Science 315, 115-119 (2007). (How FRET and FLIF are used to study enzyme-substrate complexes).
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Microscopy and Imaging (commercial reference sites) |
Cellomics |
High content screening platforms. Part of Fisher Scientific. |
Chroma |
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) |
Glen Spectra |
Filters, fibre optics etc |
Hamamatsu |
CCD cameras, light sources, lasers, fibre optics etc. |
Ibidi |
Special microscopy slides |
Leica |
Short descriptions on Leica's products |
| Lightools Research |
In vivo, whole animal, and macro imaging systems |
LSM Technologies |
Accessories for Zeiss Laser Scanning Microscopes |
MAG Biosystems |
This group that includes Photometrics, Qimaging, Media Cybernetics, and Optical Insights offers free web seminars |
MatTek |
Glass bottom culture dishes for live cell imaging |
Microscopy from the very beginning |
Excellent publication by Zeiss on microscopy. Author Dr. H. G. Kapitza |
MoBiTec |
MFP fluorescent dyes for labeling of biomolecules, DY dyes, and other fluorescence technology and immunohistochemistry products |
Nikon |
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. Next deadline is April 30, 2007. |
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 |
Omega |
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 UltraView LCI web page |
Concise information on UltraView |
Photonics |
News, events, products, and suppliers for microscopy and imaging. Buyer's guide, dictionary. Free magazines: Photonics Spectra, Biophotonics, Europhotonics. |
Thales Optem |
Advanced optical components and imaging applications |
| TILL Photonics |
Fluorescence live cell microscopy |
Xenogen (part of Caliper Life Sciences) |
In vivo imaging systems for whole mice and rats (bioluminescence or fluorescence) |
Zeiss Microscopy & Image Analysis web page |
Information on Zeiss products. Includes an interactive fluorophore database that allows you to superimpose the excitation and emission spectra of multiple fluorophores |
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Microscopy and Imaging (non-commercial reference sites) |
| FRETImaging.org |
Resources for FRET imaging, including FRET email listserver. |
Integrated Technologies for In-Vivo Molecular Imaging |
The goal of the Molecular Imaging Integrated Project is to generate and apply novel advanced technology for non-invasive imaging of biomolecular function in living systems ranging from single cells to whole animals. Public events, workshops, and training courses. |
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
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Purdue Powerpoint Lecture Slide Sets by Dr. J. Paul Robinson (PUCL) and others |
Powerpoint lectures from the principles of microscopy to applications of confocal microscopy. Also includes lectures on flow cytometry |
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| EAMNET (European Advanced Light Microscopy Network) |
EAMNET is a EU funded network of eight european laboratories and two industrial partners working in the field of light microscopy. The aim of EAMNET is to assist scientists in exploiting the power of imaging by organizing practical teaching courses, creating online teaching modules and offering software packages for microscopy. |
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.
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| EMIL (European Molecular Imaging Laboratories) |
EMIL is a Network of Excellence assembling European Molecular Imaging Laboratories for combating cancer. EMIL coordinates research efforts in Molecular Imaging of Cancer in Europe of Europe of 59 groups from universities, research centres and industry.
EMIL has six Technological and Training Platforms for Training and Education, scientific exchanges emulation, industrial partnerships and researchers mobility.
EMIL promotes training courses, summer schools and specialized workshops |
| Imaging&Microscopy blog |
Imaging & Microscopy journals weblog, published by GIT Verlag, A Wiley Company in Darmstadt, Germany. The place for all the latest news from the microscopy community. |
| Nordic Imaging Network |
The coopreative network of Nordic imaging in medicine and biology |
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Fluorophores and other molecular/cell biology products |
| Antibodies-online |
An antibodies marketplace |
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Clontech |
Novel Fluorescent Proteins etc. Part of Takara Bio. |
BioSupplyNet |
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 |
Evrogen |
Photoactivable fluorescent proteins etc. |
Fluorescent Spectra |
A large database by Carl Boswell and George McNamara with more than 350 fluorescent proteins listed |
Invitrogen |
Sells e.g. Molecular Probes products, Zymed immunodetection reagents, Qdots, and antibodies |
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. |
MoBiTec |
MFP fluorescent dyes for labeling of biomolecules, DY dyes, and other fluorescence technology and immunohistochemistry products |
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). |
PlanetGene |
R. Tsien's fluorescent proteins, also as fusions with other genes (more than 25000 human genes available). The fluorescent tag may be ordered as either an N- or C-terminal fusion. |
Richard-Allan Scientific |
Histology, cytology, and immunohistochemistry reagents |
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. |
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Antibodies as well as other immunohistochemistry /immunofluorescence products
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Free imaging software |
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AxioVision LE |
Software for viewing and simple processing of Zeiss ZVI image files. (Windows) |
BioImageXD |
Free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images. First beta version available. |
CellProfiler |
CellProfiler is a free open source software designed to quantitatively measure phenotypes from thousands of images automatically. |
FreeSFP |
FreeSFP is a free of charge volume renderer that enables you to explore 3D digital images instantly from a selectable viewpoint. It is especially suitable for single or multi-channel images from microscopes or MRI. The renderer is the elementary version of SVI's high end volume renderer FluVR (Fluorescence Volume Renderer).
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Gnuplot |
Command-line driven interactive data and function plotting utility |
ImageJ |
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 |
ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats |
ImageStabilizer |
ImageJ plugin that corrects x-y movement of images in time-lapse image stacks |
ImageSurfer |
3D visualization and analysis (e.g. volume rendering, 3D ROIs) |
Kyoto Encyclopedia of Genes and Genomes |
KEGG is a 2-D visualization tool for metabolic pathways |
LSM Image Browser |
Browser for Zeiss LSM confocal microscopy image files. (Windows) |
MayaVi |
Scientific data visualizer |
MBF ImageJ for Microscopy |
Continuation of WCIF ImageJ; collection of plugins and macros, e.g. bleach correction for image stacks. |
µManager |
An open source software for image acquisition. ImageJ compatible user interface. Matlab programs can be utilized in Micro-Manager. (Windows, Mac, Linux). |
MIPAV |
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 |
Osiris |
Osiris is a viewer for Papyrus / DICOM images (the actual standard for viewing, storing acquiring, communicating radiological and non-radiological medical images). It was developed at the Digital Imaging Unit (UIN) of the Service for Medical Computing (SIM) of the Radiology department of the University Hospitals of Geneva (Switzerland). |
TurboReg |
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. |
VisBio |
VioBIo is designed for visualization and analysis of multidimensional image data (Windows, Mac, Linux) |
VolumeJ |
ImageJ plugin for volume rendering by Michael D. Abramoff. |
Voxx |
Voxel-based real-time 3D image processing and rendering of multi-channel 3D and 4D data. (Windows, Mac OS X, Linux) |
XnView |
Utility for viewing and converting image files. (Windows, Mac OS X, Linux) |
XuvTools |
For stitching large 3D datasets |
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Imaging software |
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AutoQuant |
Deconvolution, visualization and analysis software for microscopy images. Web site contains basic information about deconvolution. Also a link to Clearing up Deconvolution, an article by Biggs and Kolbe - recommended reading for everyone interested in deconvolution |
Bitplane |
ImarisXT and other imaging software. Free 30 day trial for Imaris Demo |
Intelligent Imaging Innovations |
Slidebook software for image acquisition and analysis |
MediaCybernetics |
Image-Pro Plus and other imaging software |
Reindeer Graphics |
Image processing and measuring, compatible with Mac OS X and Windows |
Scanalytics |
Image acquisition and analysis, compatible with Mac OS X and Windows |
Scientific Volume Imaging |
Huygens deconvolution software, also FluVR volume rendering software |
Soft Imaging System |
Olympus imaging software company that also offers microscopes |
Universal Imaging |
MetaMorph and other image acquisition and analysis software |
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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) |
| Biomedicum Cell Imaging Cluster |
Biomedicum Cell Imaging Cluster (BCIC) |
| Helsinki Functional Imaging Center |
Coordinates the imaging activities in the Helsinki area |
Microscopic Imaging Core Facility |
Biocenter Oulu |
