The included code is a companion to the manuscript (In submission) and provides a method for transformation and resolution of both, locally discrete, and mean cellular deformation strains across single cells or networks given a known far-field strain. The code also includes an image-processing workflow, part of which takes advantage of the freely available NeuronStudio software to make neuron tree structures.
- Intel Core i7-4790K CPU,
- 16 GB memory,
- Matlab version R2015b or newer,
- Windows 10
- Matlab
- NeuronStudio (available at http://research.mssm.edu/cnic/tools-ns.html)
- TecPlot
- (other 3D viewers or Matlab's native viewer may be used.)
Please refer to NeuronStudio documentation for related installation instructions. The rest of the code does not need installing. Place it in your working directory.
Example Data The data is already in .mat format. Since there is no needed bioformat to mat conversion, block 2 of ProcessRunFile can be skipped. We recommend keeping the data in the folder matching in name because the code expects that architecture.
The expected output should be a processed .tiff file, an .swc file output from NeuronStudio, a segmented.tiff file, and a .plt file for optional import into TecPlot
Expected run time varies by dataset. Processing of included demo data set on a computer with recommended system requirements resulted in the following run times:
- ProcessRunFile: 0.7s (without FIDVC drift correction)
- MaskRunFile: 4.1s
- StrainRunFile: 0.9s (without plotting)
- BlebStrainRunFile: 1.6s
The FIDVC (optional block, code not included. Download FIDVC code from our Github page) and bfmatlab folders need to be in the search path in order to run all blocks of ProcessFunFile.
Please refer to the manuscript text or comments within the code for detailed instructions on how to run it. Also refer to Questions/Issues. Add a new question if similar issue hasn't been reported. We shall help you at the earliest. The author's contact information can be found at Franck Lab.