Matlab packages for raw PALM/STORM image data processing
The Nan Lab uses their own custom software packages for PALM/STORM data processing. These packages have been used in our previous publications and are still being actively developed and maintained. They are currently provided as is, but we wish to provide regular updates on these software packages, including adding more functionalities and detailed user instructions. These have been tested on a Linux server running Ubuntu LTS 12.04 x86_64 and Matlab R2013a.
If you find these packages or some of the functions helpful, feel free to use them in your research (and cite our paper, Nan et al., PNAS 2013).
- WFIRead – package for analyzing raw PALM/STORM images to generate particle coordinates.
- Note 1: Particle finding and Gaussian fitting functions were written in C, which makes them fast but you will need to recompile the .c (mex) functions for your specific platform before you could run the software. The Gaussian fitting function also requires the lapack libraries.
- Note 2: The package uses BioFormats to open OME TIF files. Please visit the OME developers website to obtain the most recent version of the Bioformats package for Matlab, and place it in the subfolder 'loci' after unzipping.
- PALM – package for sorting particle coordinates, rendering, and cluster analysis
- Note: Some of the routines were also written in C to speed the program up, so you may need to recompile the .c files to run the palm program.
Nan Lab plasmids on Addgene
Addgene is a nonprofit plasmid repository for communal sharing of genetic material. We frequently request plasmids from Addgene for our research and also deposit most of our published plasmids to Addgene for sharing with other researchers. The current list of plasmids shared through Addgene is as follows:
- pENTR-D-TOPO-PAmCherry1-MCS (Addgene 60608) This plasmid is an entry clone with the PAmCherry1 coding sequence flanked by multiple cloning sites (although we typically use it with the InFusion kit). It is made for creating fusion proteins to PAmCherry1 with flexibility. (Nan et al., PNAS, 2013.)
- pENTR-D-TOPO-PAmCherry1_1-159-MCS (Addgene 60545) The N-fragment of PAmCherry1 for BiFC and BiFC-PALM applications (Nickerson et al., PLoS One, 2014.)
- pENTR-D-TOPO-PAmCherry1_160-236-MCS (Addgene 60546) The C-fragment of PAmCherry1 for BiFC and BiFC-PALM applications (Nickerson et al., PLoS One, 2014.)