CCI – Centre for Cell Imaging

Useful Links

Useful links:

General
– Research integrity and Image processing (html)
– Microscopy resources- microlist.org or microscopy.info
– Tips for light microscopy (University of Chicago, IMCF, pdf)
– Life Technologies – Handbook (html)

Educational:
– e-learning: iBiology BioChemWeb
– Collected image analyses (imagescience.org)
– Super Resolution WIKI  / STORM WIKI /  OMX SIM WIKI
– Basics in Microscopy (PDF, Dr. Arne Zeitz,  EPFL, Lausanne) /
Molecular expressions
Nikon Microscopy 4U
Zeiss online campus
Olympus microscopy resource center
Leica Science lab

Societies:
– Bioimaging Utrecht (BUI)
– Utrecht life Sciences (ULS)
– Nederlandse Vereniging voor Microscopie (NVvM)
– European Microscopy Society (EMS)
– Royal Miroscopy Society (UK)
– Microscopy Society of America (MSA)

Fora:
Confocal Microscopy List
ImageJ
– Image freeware forum- image.sc (FIJI, ICY, Cell Profiler etc.) –
– ImageJ User Guide (
html)
ImageJ tutorial by Peter Bankhead Queens Univ. Belfast (2014)
– Bitplane Imaris forum / tutorials

Spectra of fluorochromes:
FPbase
– Life Technologies Spectra viewer
BD Fluorescence Spectrum Viewer
Chroma spectra viewer
Fluorescent dye spectra (Univ. Arizona)
Evrogen spectra viewer (for fluorproteins)
– More in Fluorophores.org (Univ. Graz)

Manufactures:
Microscopes: Leica / Nikon / Zeiss / Evident / Perkin elmer / API / 3i / Bruker / CrestOptics / Confocal.nl /
Cameras: Andor / Photometrics / Hamamatsu
Filters: ChromaSemrock / Thorlabs
Lenses: NIKON /ZEISS/ LEICA/ Evident
Imaging Chambers:

ManufacturerDish format 35 mmSlide format
Ibidi (many formats, check site, recomm. glass bottom)8115881817 (18w)
Greiner CellView 627870 (4w)543078 (10w)
WPI- FluorodishFD35-100 / FD35-10
Thermo Attofluor 25 mm coverslip holderA7816
Nunc LabTek II (odd format – poor fit in holders) 155409PK (8w)
MatTek (35 mm dish)P35G-15-14C
CellVis (18 well slide)C18-1.5H (18w)

Image Dbase management
– Open Microscopy Environment (OME)
– Center for Bio-image Informatics (Bisque)

General:
– Reference managing: Mendeley (no longer open source) / Zotero
– Lab inventory management: Quartzy
– eLabJournal: Benchling / RSpace / Notion / Joplin

Molecular biology:
– vector exchange:       Addgene / Kerafast
– sequence analyses:   Snapgene / Serial cloner / Genecompiler / Benchling / ApE