# BFPTool

A Matlab based tool with GUI designed to process and analyse videos recorded during Biomembrane Force Probe (BFP) experiments. It allows post-experimental selective video processing, calculations and analysis of the results. Supplementary tools like import/export, visualizations and in-video measurements were implemented.
The uderlying methods, implementation, and typical use are described in the article: Smit et al., BMC Biophysics 10:2 (2017), DOI: 10.1186/s13628-016-0033-2

## Getting Started

The installation of the tool is simple. Repository contains BFPTool.mlappinstall file, which allows direct installation into Matlab as an external app. Matlab unpacks the source files and documentation into Matlab App directory, the source M-files can be modified there.

### Prerequisites

The software runs under Matlab (tested on 2015a and newer) with Image Processing Toolkit. It was tested so far under Linux (Ubuntu 16.04), Windows 10 and Mac OS 10.9 and later.

### Installation

Application can be installed into Matlab application dashbar. Click the button Install App on the Apps tab and browse to the BFPTool.mlappinstall file. An icon to the app appears on the dashbar.

Repository also contains source M-files, BFPGUI.m, BFPClass.m, TrackBead.m, TrackPipette.m, vidWrap.m and BackDoor.m. These files contain the full code (without documentation) and are sufficient to run the application and modify it. No installation is necessary, the files just need to be in a directory on the Matlab path.

The folder /html contains M-files used to generate the Documentation and the Documentation itself. If the app is installed through MLAPPINSTALL file, the documentation is automatically loaded (during the first application run) into the Matlab help interface and is fully searchable.

## Running the app

The program can be run either from the Matlab dashboard (if installed through the interface) or started by running the BFPGUI.m file. It initialized the GUI. There is no need for any particular settings. The Documentation covers a short (and a bit extended) guide to get started.

### Testing material

The repository contains a folder /testvideo which contains recorded footage from BFP experiments. Users can use this footage to learn how to use the tool. The file 'basic.avi' can be analysed without detailed settings of the GUI. The other two files 'interrupted.avi' and 'multiinterval.avi' help user to see why some of the settings and features are necessary. The Documentation contains a step-by-step guide, which can be used with these videos (tested).

## State of the program and cooperation

The program has been tested and is robust for the most of conceivable use. More tests on unlikely or illogical combinations or sequences of steps would be very helpful. The program was also being implemented gradually with emphasise on functionality and robustness, coding elegance was not a priority. Particularly sections of GUI could be improved, having several functions merged into one.

### Scientific community

This program is dedicated to the scientific community working (or willing to work) with the BFP technique. For anyone else, any form of use is hard to imagine.

## License information

This program 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.

    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.

## Authors

* initial work was done by Daniel Smit, with intensive testing by Mohamed Doulazmi

## Acknowledgements

* many helpful comments and ideas came from Alain Trembleau and Martin Zapotocky
* initial ideas as how to treat the videos, which eventually led to the development of the application must be contributed to Frederic Pincet
* thanks also go to Nicolas Debray for help with testing
* development of this software was supported by the Czech Science Foundation grant 14-16755S