wfxue / trace_y

Trace_y

Tracing and individual filament 3D structural analysis and an app for AFM image analysis

Reference (pre-print): Xue, W.-F., Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy. bioRxiv, 2023.07.05.547812 (2023). https://doi.org/10.1101/2023.07.05.547812

Contact

Wei-Feng Xue mailto:[email protected]

Relevant publications:

Aubrey, L. D., Lutter, L., Fennell, K., Purton, T. J., Ward, N., Serpell, L. C., Xue, W.-F. Structural reconstruction of individual filaments in Abeta42 fibril populations assembled in vitro reveal rare species that resemble ex vivo amyloid polymorphs from human brains. bioRxiv, 2023.07.14.549001 (2023). https://doi.org/10.1101/2023.07.14.549001

Lutter, L., Al-Hilaly, Y. K., Serpell, C. J., Tuite, M. F., Wischik, C. M., Serpell, L. C. & Xue, W.-F. Structural Identification of Individual Helical Amyloid Filaments by Integration of Cryo-Electron Microscopy-Derived Maps in Comparative Morphometric Atomic Force Microscopy Image Analysis. J Mol Biol 434, 167466, (2022). https://doi.org/10.1016/j.jmb.2022.167466

Aubrey, L. D., Blakeman, B. J. F., Lutter, L., Serpell, C. J., Tuite, M. F., Serpell, L. C. & Xue, W.-F. Quantification of amyloid fibril polymorphism by nano-morphometry reveals the individuality of filament assembly. Commun Chem 3, (2020). https://doi.org/10.1038/s42004-020-00372-3

Lutter, L., Serpell, C. J., Tuite, M. F., Serpell, L. C. & Xue, W.-F. Three-dimensional reconstruction of individual helical nano-filament structures from atomic force microscopy topographs. Biomol Concepts 11, 102-115, (2020). https://doi.org/10.1515/bmc-2020-0009

Usage in matlab

>>Trace_y('-m');

Subsequently for the simple 'functions' GUI:

>>Trace_y;

Example

Example_Height_Image.csv is an example that can be loaded using the Import CSV functionality with the default image size parameters.

Executable versions

Compiled with matlab compiler (see compiler notes below): Trace_y.exe (Win) Trace_y.app (Mac)

Prerequisites for Deployment

Verify that version 9.12 (R2022a) of the MATLAB Runtime is installed.
If not, you can run the MATLAB Runtime installer. To find its location, enter

>>mcrinstaller

at the MATLAB prompt. NOTE: You will need administrator rights to run the MATLAB Runtime installer.

Alternatively, download and install the Macintosh version of the MATLAB Runtime for R2022a from the following link on the MathWorks website:

https://www.mathworks.com/products/compiler/mcr/index.html

For more information about the MATLAB Runtime and the MATLAB Runtime installer, see "Distribute Applications" in the MATLAB Compiler documentation
in the MathWorks Documentation Center.

Definitions

For information on deployment terminology, go to https://www.mathworks.com/help and select MATLAB Compiler > Getting Started > About Application Deployment > Deployment Product Terms in the MathWorks Documentation Center.

License

MIT License

Copyright (c) 2023 wfxue (Wei-Feng Xue)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.