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Bioenergy & Defense

Bioenergy & Defense Technologies

Software

Sandia Simple Particle Tracking (Sandia SPT) v 1.0

Download (Matlab Code)

Sandia SPT is intended to provide an easy to use single particle tracking implementation, including source code for all the required steps (spot detection, localization, and linking observations). This software was developed as part of a book chapter1 introducing the reader to techniques to fluorescently label individual proteins in living cells and extract their quantitative dynamics. As such, algorithms were selected for their ease of use and understandability, not necessarily to represent the state of the art. Please see the book chapter for more detailed information and instructions on how to use Sandia SPT.

  1. Anthony, S.M.; Carroll-Portillo, A.; Timlin, J.A., Dynamics and Interactions of Individual Proteins in the Membrane of Living Cells. In Anup K. Singh (Ed.) Single Cell Protein Analysis Methods in Molecular Biology. Spinger 2015, 185-207

License Info

Copyright 2014 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. Sandia SPT is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Sandia SPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Sandia SPT. If not, see http://www.gnu.org/licenses/.

Sandia Hyperspectral Upper-Bound Spectrum (Sandia Hyper-UBS) v 1.0

Download (Matlab Code)

Sandia Hyper-UBS is designed to remove cosmic ray spikes from hyperspectral data sets. This software was based upon the UBS-DM algorithm by D.M. Zhang and Do Ben-Amotz.1 The UBS-DM-HS algorithm is designed to be more robust and is better at removing cosmic ray spikes which impact multiple pixels. See the associated journal article2 for more details. Sandia Hyper-UBS also provides implementations of the other algorithms tested in the journal article.

  1. Zhang, D. M. and D. Ben-Amotz, "Removal of cosmic spikes from hyper-spectral images using a hybrid upper-bound spectrum method" Applied Spectroscopy 2002, 56(1): 91-98.
  2. Anthony, S.M. and Timlin, J.A., “Removing Cosmic Spikes Using a Hyperspectral Upper-Bound Spectrum Method” Applied Spectroscopy 2016

License Info

Copyright 2016 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software.

Sandia SPT is free software released under the BSD license. The full text of the license is included in the download or the terms of the license can be seen at https://opensource.org/licenses/BSD-3-Clause.

 

 

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