Resources

Matlab packages for raw PALM/STORM image data processing

The Nan Lab uses both third-party software (such as SMAP and DECODE, among others) and our own custom packages for PALM/STORM data processing. Our custom software packages have been used in essentially all of our publications and still being actively developed and maintained. At present, the packages comprise wfiread and palm, both developed in MatLab with key functions written in C for speed under Linux (running as a headless server).

Both packages have been deposited on GitHub. Both have been tested on Ubuntu LTS 18.04 running MatLab 2019a and above.

If you find these packages or some of the functions helpful, feel free to use them in your research (and cite our recent paper, Koester et al. Current Protocols, 2022).

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 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.)
     
  • pLenti-TO/CMV-DD-PAmCherry1-KRas G12D (Addgene 177320). This is an lentiviral plasmid for expressing a dimerizable KRas G12D fusion protein under Doxycycline (Dox). The gene insert here is PAmCherry1-tagged human KRAS G12D with an N-terminal dimerization domain (DD). The DD domain is a ~12 KD peptide that can be artificially dimerized using a small molecule dimerizer (e.g. AP20187, aka the B/B homo-dimerizer). With the use of a Tet-ON (TO) / CMV promoter, expression of the gene insert is induced with doxycycline (Dox) if the host cell expresses the tet-repressor (tetR). See details in our publication (Nan et al. PNAS, 2015).
     
  • 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.)