BNP-Track

This software package includes several Matlab scripts and auxiliary functions, which implement the computational algorithms for the framework BNP-Track described in: https://www.nature.com/articles/s41592-024-02349-9

Prerequisites

Our code requires Matlab and its Statistics and Machine Learning Toolbox.

Downloading BNP-Track

You can download our code by cloning the git repository:

git clone https://github.com/LabPresse/BNP-Track.git

Alternatively, GitHub allows users to download a repository as a tarball or zipball. Check here for more details.

Using BNP-Track

1. Once BNP-Track is downloaded (and extracted), open Matlab and navigate to the folder containing all source files.
2. To get a quick start with GUI, please run BNP_Track_app in the Matlab command window.
3. If finer control is preferred, please open BNP_track_driver.m, directly modify the parameters there, then run this file.
4. Please refer to our manuscript and this documentation for more details.

Further Assistance

We are working on the implementation and documentation of BNP-Track. You are highly encouraged to contact us at [email protected] or [email protected] for help! Issues and pull requests are also very much appreciated!

Workarounds

We seek to address issues directly, but this takes time. Therefore, we list some quick workarounds here for these issues.

1. Currently, BNP-Track only supports reading image stacks that are already stored as a 3D array in Matlab. However, many users have their frames in the TIFF format. To help import the data, we provide tiff2mat.m, which reads an image stack from a TIFF file¹. We also offer mat2tiff.m, which is the inverse of tiff2mat.m.

Footnotes

1. The orientation of an image may be changed when loaded using tiff2mat.m. ↩