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* [http://support.svi.nl/wiki/NyquistCalculator Nyquist Calculator]<br>calculate the - according to Harry Nyquist - perfect sampling for your setup | * [http://support.svi.nl/wiki/NyquistCalculator Nyquist Calculator]<br>calculate the - according to Harry Nyquist - perfect sampling for your setup | ||
| − | + | === Sample mounting === | |
| − | * [https:// | + | * How to [https://www.biodip.de/wiki/Sample_mounting mount samples] for high resolution microscopy? |
| + | * Which [https://ifn.mpi-cbg.de/wiki/ifn/index.php/Coverslips Coverslips] to use for microscopy? | ||
=== CCD cameras === | === CCD cameras === | ||
| − | * [http://www.photometrics.com/resources/learningzone/ Photometrics learning zone] <br> nice collection about all kind of information concerning CCD cameras. Note: Photometrics offers a cost free, 2-day camera course, which is run every 3 | + | * [http://www.photometrics.com/resources/learningzone/ Photometrics learning zone] <br> nice collection about all kind of information concerning CCD cameras. Note: Photometrics offers a cost free, 2-day camera course, which is run every 3 months in the UK |
== Spectral & Optical Data == | == Spectral & Optical Data == | ||
| − | [[image:Invitrogen-spectra.jpg|thumb|Invitrogen Spectra Viewer [http:// | + | [[image:Invitrogen-spectra.jpg|thumb|Invitrogen Spectra Viewer [http://www.lifetechnologies.com/greater-china/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html.html link]]] |
[[image:Onlinespectraviewer.png|thumb|Online Spectra Viewer: full setup for acquisition of eGFP [http://www.online-spectra.com/applet.html link]]] | [[image:Onlinespectraviewer.png|thumb|Online Spectra Viewer: full setup for acquisition of eGFP [http://www.online-spectra.com/applet.html link]]] | ||
=== Fluorochrome Spectra === | === Fluorochrome Spectra === | ||
| − | * [http://www. | + | * [http://www.spectra.arizona.edu/ Fluorescent Spectra Database by Carl Boswell, Urs Utzinger]<br>comprehensive database with sorted spectras and lasers, lamps and filter sets |
| − | * [http:// | + | * [http://www.lifetechnologies.com/de/de/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html Invitrogen Fluorescence Spectra Viewer]<br>nice layout, no search function, Java based |
| − | + | ||
| − | + | ||
* [http://www.bdbiosciences.com/spectra BD Biosciences Fluorescence Spectrum Viewer]<br>slightly different fluorochrome setup, i.e. some FACS dyes | * [http://www.bdbiosciences.com/spectra BD Biosciences Fluorescence Spectrum Viewer]<br>slightly different fluorochrome setup, i.e. some FACS dyes | ||
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=== Filter Specifications === | === Filter Specifications === | ||
| − | * [http://www.ahf.de/ | + | * [http://www.ahf.de/optical_filter_systems.html AHF Analysentechnik Filtersystems] |
*[http://www.aic-imagecentral.com/products/pdfs/hdbk4.pdf Chroma Technology Corp Handbook of Optical Filters for Fluorescence Microscopy] | *[http://www.aic-imagecentral.com/products/pdfs/hdbk4.pdf Chroma Technology Corp Handbook of Optical Filters for Fluorescence Microscopy] | ||
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* [http://microscope.olympus.com/uis2/ Olympus objective database] | * [http://microscope.olympus.com/uis2/ Olympus objective database] | ||
| − | * [http://www.nikon.com/products/instruments/lineup/biological-microscopes/accessory/ | + | * [http://www.nikon.com/products/instruments/lineup/bioscience/biological-microscopes/accessory/objectives/index.htm Nikon objective list] |
| + | |||
| + | * [[media:Objective specifications.jpg|Objective specifications]] | ||
| + | |||
| + | === Refractive Index=== | ||
| + | Measurements were performed at MPI-CBG LMF, with the J457 Automatic Refractometer (RUDOPLH) for each medium, in a temperature range between 10 and 60 Celsius degrees at 1 degree steps. | ||
| + | * [[media:Immersion oil.pdf|Immersion Oil]] | ||
| + | |||
| + | * [[media:Immersion water.pdf|Immersion Water]] | ||
| + | |||
| + | * [[media:Silicone.pdf|Silicone Immersion Oil]] | ||
| + | |||
| + | * [[media:Glycerol type G leica.pdf|Glycerol Type G]] | ||
| + | |||
| + | * [[media:Glycerol 100%.pdf|Glycerol 100%]] | ||
| + | |||
| + | * [[media:Glycerol 50%.pdf|Glycerol 50%]] | ||
| + | |||
| + | * [[media:Ultrasonic Gel.pdf|Ultrasonic Gel]] | ||
| + | |||
| + | * [[media:Vidisic.pdf|Vidisic]] | ||
== Free Software == | == Free Software == | ||
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=== Image Acquisition === | === Image Acquisition === | ||
| − | *[http://micro-manager.org/ µManager]<br>open source software package for imaging and control of automated microscopes, refer to the [ | + | *[http://micro-manager.org/ µManager]<br>open source software package for imaging and control of automated microscopes, refer to the [https://micro-manager.org/wiki/Overview%20of%20the%20documentation µManager documentation] for configurations etc.<br>(Windows, Mac OS, Linux) |
=== Image Processing and Analysis === | === Image Processing and Analysis === | ||
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* [[Fiji|Fiji / ImageJ]]<br>open-source software for microscopy-related tasks | * [[Fiji|Fiji / ImageJ]]<br>open-source software for microscopy-related tasks | ||
| − | + | * [http://www.bioimagexd.net/ BioImageXD]<br>open-source image analysis software<br>(cross platform) | |
| − | + | ||
| − | * [http://www.bioimagexd.net/ BioImageXD]<br>open-source image analysis software<br>( | + | |
| − | * [http:// | + | * [http://microscopy.zeiss.com/microscopy/en_de/website/downloads/download-zen-le.html Zeiss ZEN LE]<br>new free Zeiss software for viewing and processing *.lsm images<br>(Windows XP 32bit, Windows 7 32/64 bit) |
| − | * [http://www.zeiss. | + | * [http://www.zeiss.com/microscopy/en_de/website/downloads/lsm-image-browser.html Zeiss LSM Image Browser]<br>traditional free Zeiss software, can open database (*.mdb) and images (*.lsm) including all comments and acquisition information<br>(Windows only) |
* [ftp://ftp.llt.de/softlib/LAS_AF_Lite/ Leica LAS AF Lite]<br>free Leica software, can open *.lif and *.lei files, acquisition information are accessible<br>(Windows XP 32bit only) | * [ftp://ftp.llt.de/softlib/LAS_AF_Lite/ Leica LAS AF Lite]<br>free Leica software, can open *.lif and *.lei files, acquisition information are accessible<br>(Windows XP 32bit only) | ||
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* [http://downloads.olympus-europa.com/microscopy/software/FV_Viewer.exe Olympus FV Viewer]<br>free Olympus software, can open *.oib and *.oif files from Fluoview Confocals<br>(Windows XP 32bit only) | * [http://downloads.olympus-europa.com/microscopy/software/FV_Viewer.exe Olympus FV Viewer]<br>free Olympus software, can open *.oib and *.oif files from Fluoview Confocals<br>(Windows XP 32bit only) | ||
| − | * [http:// | + | * [http://microscopy.zeiss.com/microscopy/de_de/downloads/axiovision.html Zeiss Axiovision LE]<br>free version of the Axiovision software, able to open *.lsm files as well, nice batch export<br>(Windows only) |
* [http://www.irfanview.com/ IrfanView]<br>image viewer for common file formats like *.tif and *.jpg, provides simple processing and batch conversion, slide show etc.<br>(Windows only) | * [http://www.irfanview.com/ IrfanView]<br>image viewer for common file formats like *.tif and *.jpg, provides simple processing and batch conversion, slide show etc.<br>(Windows only) | ||
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*[http://www.till-photonics.com/ TILL Photonics]<br>iMIC, Polychrome | *[http://www.till-photonics.com/ TILL Photonics]<br>iMIC, Polychrome | ||
| − | *[http://www. | + | *[http://www.perkinelmer.com/pages/020/cellularimaging/improvision/default.xhtml Improvision]<br>Volocity |
*[http://www.bitplane.com Bitplane]<br>Imaris | *[http://www.bitplane.com Bitplane]<br>Imaris | ||
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*[http://cores.imp.ac.at/biooptics/ IMP Vienna, BioOptics Facility] | *[http://cores.imp.ac.at/biooptics/ IMP Vienna, BioOptics Facility] | ||
*[http://www.mcgill.ca/lifesciencescomplex/core/imaging/ McGill University Life Sciences Complex Imaging Facility] | *[http://www.mcgill.ca/lifesciencescomplex/core/imaging/ McGill University Life Sciences Complex Imaging Facility] | ||
| − | *[http://www.ipk-gatersleben.de/ | + | *[http://www.ipk-gatersleben.de/en/dept-physiology-and-cell-biology/structural-cell-biology/microscopy-core-facility/ The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) - Structural Cell Biology Group - core facility] |
*[http://www.lmc.ethz.ch LMC Zürich] | *[http://www.lmc.ethz.ch LMC Zürich] | ||
| − | *[http://www.nki.nl/ | + | *[http://www.nki.nl/ Amsterdamm NL - Rob Wolthuis r.wolthuis at nki.nl] |
Latest revision as of 13:17, 13 October 2015
Contents |
[edit] Microscopy - Infos and Introductions
- Molecular Expressions Microscopy Primer
very comprehensive - provides information about various microscopy techniques, stainings and much more- Nikon MicroscopyU
Nikons part of the MEM Primer - Olympus Microscopy Resource Center
Olympus' part of the MEM Primer
- Nikon MicroscopyU
- Carl Zeiss MicroImaging Campus
tutorials about microscopy and digital imaing offered by Carl Zeiss company
- Nyquist Calculator
calculate the - according to Harry Nyquist - perfect sampling for your setup
[edit] Sample mounting
- How to mount samples for high resolution microscopy?
- Which Coverslips to use for microscopy?
[edit] CCD cameras
- Photometrics learning zone
nice collection about all kind of information concerning CCD cameras. Note: Photometrics offers a cost free, 2-day camera course, which is run every 3 months in the UK
[edit] Spectral & Optical Data
[edit] Fluorochrome Spectra
- Fluorescent Spectra Database by Carl Boswell, Urs Utzinger
comprehensive database with sorted spectras and lasers, lamps and filter sets
- Invitrogen Fluorescence Spectra Viewer
nice layout, no search function, Java based
- BD Biosciences Fluorescence Spectrum Viewer
slightly different fluorochrome setup, i.e. some FACS dyes
- Online Spectra Viewer
a lot of dyes, filters and lasers available, rather simple layout
- Fluorophores.org by TU Graz
extensive database with spectras, lifetimes etc.
[edit] Filter Specifications
- AHF Analysentechnik Filtersystems
- Chroma Technology Corp Handbook of Optical Filters for Fluorescence Microscopy
[edit] Objective Data
[edit] Refractive Index
Measurements were performed at MPI-CBG LMF, with the J457 Automatic Refractometer (RUDOPLH) for each medium, in a temperature range between 10 and 60 Celsius degrees at 1 degree steps.
[edit] Free Software
[edit] Image Acquisition
- µManager
open source software package for imaging and control of automated microscopes, refer to the µManager documentation for configurations etc.
(Windows, Mac OS, Linux)
[edit] Image Processing and Analysis
- Fiji / ImageJ
open-source software for microscopy-related tasks
- BioImageXD
open-source image analysis software
(cross platform)
- Zeiss ZEN LE
new free Zeiss software for viewing and processing *.lsm images
(Windows XP 32bit, Windows 7 32/64 bit)
- Zeiss LSM Image Browser
traditional free Zeiss software, can open database (*.mdb) and images (*.lsm) including all comments and acquisition information
(Windows only)
- Leica LAS AF Lite
free Leica software, can open *.lif and *.lei files, acquisition information are accessible
(Windows XP 32bit only)
- Olympus FV Viewer
free Olympus software, can open *.oib and *.oif files from Fluoview Confocals
(Windows XP 32bit only)
- Zeiss Axiovision LE
free version of the Axiovision software, able to open *.lsm files as well, nice batch export
(Windows only)
- IrfanView
image viewer for common file formats like *.tif and *.jpg, provides simple processing and batch conversion, slide show etc.
(Windows only)
[edit] Mailing Listserver
- The Microscopy Listserver
mailing list for all topics related to microscopy, but with a focus on electron microscopy
- Confocal List Server
Confocal Microscopy List, many subscribers and discussions, archive function
- ImageJ Mailing List
lots of discussions, good if you are interested in using ImageJ more advanced
[edit] Companies
- Carl Zeiss MicroImaging GmbH
LSM 710 and LSM 5 Live confocals, microscope frames and objectives
- Leica Microsystems
SP5(-X) and SPE confocals, microscope frames and objectives
- Olympus Microscopy
FV1000(MPE) confocal, microscope frames and objectives
- Nikon Instruments Europe B.V.
A1(R) confocal, microscope frames and objectives
- Andor Technology
Revolution, IQ software, system integration
- TILL Photonics
iMIC, Polychrome
- Improvision
Volocity
- Bitplane
Imaris
- okolab
stage incubators, cage incubators
- Ibidi
single- and multi-well dishes with cover-slip bottom, stage incubator
- Molecular Devices
MetaMorph, MetaVue
- Intelligent Imaging Innovations
FLIM, Marianas, Everest, SlideBook software, system integration
- Sutter Instrument
DG-4 lightsource, micromanipulators, accessories
- LaVision Biotec
TriMScope 2-Photon, FLIM, software, accessories
- Photometrics
cameras (CCD, EMCCD)
[edit] Our Friends and contacts
- Turku BioImaging (Finland)
- Biological imaging Development Center at UCSF
- IMP Vienna, BioOptics Facility
- McGill University Life Sciences Complex Imaging Facility
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) - Structural Cell Biology Group - core facility
- LMC Zürich
- Amsterdamm NL - Rob Wolthuis r.wolthuis at nki.nl
