Mosaic Preprocessing Pipeline

View the Project on GitHub CBlasse/premosa

Navigation

1. Introduction
2. Installation
3. Usage
4. Example

Installation

The pipeline has only been developed for Linux/ Mac OSX.

Prerequisites

For Max OSX systems:

Cmake, at least version 3.0 (get it here, please make sure it also runs from the command line)
Fiji (get it here)
Java 8

For Linux systems:

Cmake, at least version 3.0 (get it here, please make sure it also runs from the command line)
Fiji (get it here)
Java 8
xvfb (e.g. with 'sudo aptitude install xvfb')

Installation

Download the source code by using either the download page or the git repository:

git clone https://github.com/CBlasse/premosa.git

Go to the project folder and run:

./Build.sh

This step will generate executable programs in the ./bin/ folder.

Install the contrast adjustment plugin in Fiji. To do so, copy the contrastAdjustment-26.1.0.jar into the plugins folder of your Fiji distribution. To use the plugin, it is necessary to launch Fiji with Java 8.

We would like to acknowledge the C++ XML parser TinyXML, which we integrated into our software package to parse XML files.

Data example

A data example can be downloaded here.