Links

LCAM microscopy centres:

LCAM (general)
LCAM-AMC (facility) & research group
LCAM-FNWI (microscopy part) & research group
LCAM-NKI (facility) & research group

Basics in microscopy:

MyScope online microscopy course
Nikon microscopy education website
Zeiss microscopy education website
Evident (former Olympus) microscopy education website
Leica microscopy education website

Applications:

Invitrogen spectra viewer (spectra of fluorescent dyes)
FP Database (spectra and others of fluorescent proteins)
ImageJ (free image processing software)

Software:

LCAM also uses several custom-developed packages and tools that are freely downloadable.

LCAM RDM files for microscopy (available soon)
This package contains the exel-based Research Data Management files for multiple microscopes available within LCAM. These files can be used to quickly create a digital labjournal. Created: LCAM staff

LCAM LUTs
This package contains a Zipfile with various color Look Up Tables (LUTs) that are optimized for being linear in grayscale prints as well. One can download these definitions and add them to the LUT subdirectory of your ImageJ installation. Created: Marten Postma
In some cases one has images with a lot of (black) background with only a few minor fluorescence spots. In this case it’s better to use an inverse LUT where the background will become white with a colored foreground. Click here to use the ShinyApp EZReverse to quickly invert your existing images. Created: Joachim Goedhart

LCAM PTU converter
This C++ based software can convert Picoquant pt3 files into images of different format  (like tiff) in order to process the images in standard image processing software packages (like f.e. freeware ImageJ). It allows to use the time-gating properties and export images containing the full lifetime decay for each pixel. Created: Marten Postma & Mark Hink

PlotTwist
This PlotTwist Shiny app plots the data and statistics of time-dependent measurements (or other continuous data, such as spectra). The philosophy of the approach is that plotting the raw traces (instead of a summary) improves transparency and interpretation. To further facilitate the comparison, summary statistics (mean) and inferential statistics (confidence intervals) can be added. For more info click here. Created: Joachim Goedhart & Marten Postma

Plots of Data
This Shiny app plots the data and statistics to enable the comparison of (experimental) conditions. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation. To further facilitate the comparison, summary statistics (mean, median, boxplot, violinplot) and inferential statistics (confidence intervals) can be added.  For more info click here. Created: Joachim Goedhart & Marten Postma

Plots of Differences
This Shiny app plots the data, statistics and (optional) differences to enable the comparison of (experimental) conditions. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation. To further facilitate the comparison, summary statistics (mean, median, boxplot) and inferential statistics (confidence intervals) can be added. Created: Joachim Goedhart & Marten Postma

Alternative data visualisation apps
For alternative data visualisation tools multiple ShinyApps are available here. Created: Joachim Goedhart

DNA constructs:

Molecular Cytology DNA constructs: LMC Database
This Excel sheet (only for internal use) can be used to check the presence and characteristics of all DNA constructs available in the Lab of Molecular Cytology (LMC). Alternatively one can search for constructs using this Shiny App. Created: Joachim Goedhart

Molecular Cytology DNA constructs: Addgene distribution webpage
All DNA constructs that are being used in the publications of the Molecular Cytology laboratory are available via Addgene. Here one can find and order a variety of developed fluorescent proteins, organelle markers and biosensors, including sequence information. For technical details about the constructs one can contact the LCAM or Molecular Cytology staff, Construct ordering goes via Addgene only and not via the Mol. Cyto. lab.

Courses in microscopy:

UvA Masterstudy Biomedical Sciences: Cell Biology and Advanced Microscopy
Microscopycourse.nl (summary of all LCAM-related microscopy courses)

Microscopy organisations:

Nederlandse Vereniging voor Microscopy (NVvM)
NL-Bioimaging AM
Eurobioimaging
Global Bioimaging
MicroscopyDB via ELMI

University of Amsterdam:

UvA main website
Faculty of Science
Swammerdam Institute for Life Sciences
Molecular Cytology section