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
Olympus microscopy

Applications:

Invitrogen spectra viewer (spectra of fluorescent dyes)
FP Database (spectra and others of fluorescent proteins)
SIP chart analysis (calibration of your sectioning fluorescence microscope)
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 various color Look Up Tables (LUTs) that are optimized for being linear in grayscale prints as well. Created: Marten Postma

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

DNA constructs:

LMC Database
This app (only for internal use) can be used to check the presence and characteristics of all DNA constructs available in the Lab of Molecular Cytology. Created: Marten Postma

Molecular Cytology constructs
All DNA constructs that are being used in the publications of the Molecular Cytology section are available via Addgene. Here one can find a variety of developed fluorescent proteins, organelle markers and biosensors, including sequence information. For more info one can contact the LCAM or Molecular Cytology staff.

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)
Eurobioimaging
NL-Bioimaging AM

University of Amsterdam:

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