PSFTracker

Publication

The PSFtracker tool was published in the following article:

Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time.

Klemm AH, Thomae AW, Wachal K, Dietzel S.

Microsc Microanal. 2019 Jun;25(3):699-704.

Link to journal page. DOI: https://doi.org/10.1017/S1431927619000060. PMID: 30722807.

Anna H Klemm who developed the PSFtracker code is now at the Department of Information Technology at Uppsala University.

Description

PSFtracker is a tool to evaluate the point spread function of a microscopic system over time. 3D images of beads (gold or fluorescent) are first processed with the open-source software PSFj. The original images and PSFj output files from multiple evaluations over longer time periods are then used by PSFTracker to generate a visualization of PSF size and shape over time, all embedded in a web page. An example of such a page can be found here. Data for several objectives or microscopes can be processed in parallel. PSFTracker is realized in KNIME. A detailed manual is provided as supplement to the article and also can be downloaded from the links below.

Please see the article for further information.

Required software and files

The PSFTracker Package comes as a zip file which contains PSFTracker.knwf, the KNIME workflow file, sample input and sample output. We recommend to use the sample input to test if PSFTracker and the helper programs were installed correctly. Download package 2020-02-25 (33 MB).

The following two files are already included in this package:

• PSFtracker Workflow Description and Manual (Version 2020-02-25). This pdf manual starts with a step-by-step manual guiding the novice user through all required steps. It also contains information that will allow the expert user to adapt PSFtracker to new tasks.
• KNIME workflow file 20180123_PSFTracker.knwf provided as zip file.

PSFJ: We used PSFj v2.0 build 241. Newer versions may or may not be compatible with PSFtracker. Download page at the Knop lab web site. See here if you have trouble running it.

PSFtracker is a KNIME workflow file. Install KNIME Analytics Platform from www.knime.org. We used KNIME version 3.5.0 and 3.5.1 64 bit. PSFtracker probably will run under future versions. If it doesn't, try the old one. Download current version here. (Update 2020-02: 4.1.1 64 bit seems to work fine.) Download 3.5.1 here.

PSFtracker needs the software package R to draw plots. R is a free software package that provides statistical computing and graphics. Download the R Project from r-project.org and install it. We used version R-3.5.1 during development. Update 2020-02: Version 3.6.2 seems to work fine.