Bacterial exclusion prediction

A program for estimating the anti-bacterial property of surfaces based on SEM images.

This repository is administered by Shadi Rahimi (@Shadirahimi), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.

Usage

The software can be build and run without arguments using Cargo if all dependencies are installed (see "Build" section below for information about installing dependencies).

cargo run --release

This command will start a interactive web server for live configuration locally on http://127.0.0.1:8080. The interface greets the user with an analysis of the image specified in the first text field.

To learn more about the other options to the program we can run the following command, displaying a help menu describing the modes, flags and options.

cargo run --release -- --help

Build

Linux

The easiest way to compile the program is through Nix with the provided shell.nix file. After installing Nix you only have to execute the following two commands from the cloned repository to get the program built and run it.

nix-shell
cargo run --release

On other distributions you have to use your package manager for installation of Tesseract (a text recognition library). Depending on the package manager used by your distribution one of the following commands should install Tesseract when executed with root privileges.

apt install tesseract-ocr     # Debian / Ubuntu based distributions
dnf install tesseract         # Fedora / RHEL based distributions
pacman -S tesseract           # Arch Linux based distributions
zypper install tesseract-ocr  # OpenSUSE based distributions
xbps-install -S tesseract-ocr # Void Linux based distributions

When Tesseract has been installed you have to install Cargo. Read the install instruction for your particular situation but in short you can execute the following command for installation of Rustup

curl https://sh.rustup.rs -sSf | sh

There after you should be ready to build the program like other Rust projects using Cargo.

cargo run --release

MacOS

We start by launching a terminal window through Launchpad by searching for “terminal” in the search bar. Then we need to install Tesseract, which is used for text recognition. To make this easier we first install Homebrew, a MacOS package manager, by executing their installation script.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Beware the command above downloads and executes code from the internet. After Homebrew is installed by following the prompts, we can install Tesseract using the following command.

brew install tesseract

Once Tesseract is installed we have to install Cargo which is the Rust build system. It can be installed through the following command in the terminal.

curl https://sh.rustup.rs -sSf | sh

After that use Cargo to build and run the program when inside of the cloned git repository.

cargo run --release

Windows

We first install Tesseract, the text recognition software used by the program. A Windows installer can be downloaded from https://github.com/UB-Mannheim/tesseract/wiki. Run the installer with default settings and wait for it to finish.

Once Tesseract is installed, we need to open Powershell by searching for "Powershell" in the search bar of Windows. Every time we open a new Powershell window where we want to run the program we have to add Tesseract to our PATH using the following command, where the you write the path to the Tesseract installation.

$env:PATH += ";C:\Algorithm Files\Tesseract-OCR\;"

Next, Cargo has to be installed. The easiest way is through the Windows installer of Rustup downloaded from here as as stated in the install instructions. After completing the installer Rust and therefore also Cargo should be installed on your system.

Finally, enter the directory containing the cloned repository to be able to build and run the software.

cargo run --release