Welcome to ImageD

Introduction

ImageD is an image processing software.

What ImageD is intended to do/be:

• Graphical user interface
• Easy to handle for beginner users
• Lots of parametric functions for advanced users
• Multidimensional images and videos (up to 6D)
• Rapid prototyping
• Dynamic image processing chains
• Interactive image analysis
• Volumetric rendering of 3D data
• Lots of plugins for biophysics applications at GSI Darmstadt

What ImageD is not intended to do/be:

• Industrial applications like quality control
• High speed optimization

Installation

ImageD is published as OpenSource under the GPL3 licence. Its github repository can be found here.

Installation:

1. Go to https://github.com/DavidEilenstein/ImageD/releases
2. Select the version you want to dowload (click on the blue headline with v<number> in it. You can see the current version number at the top of this page)
3. Download the "ImageD_v<number>.zip"
4. Unzip it in a folder of your choice
5. Double click the ImageD.exe to run the program

Plugins

ImageD includes a lot of plugins for specific tasks, mostly in the field of biophysics:

• Cytoplasmatic dsDNA detection in fluorescence microscopy images
• Mitochondria analysis in flim images
• Cell colony size distribution measurement
• Tracking nuclear foci over time (by Manon Nickler)
• Measuring intensity profiles of ion tracks in crystals
• Multipage TIF image visualizer (false color and basic processing)
• DNA fibre thickness estimation (see below)
• Radon decay curve fitting
• Cerebral organoids size distribution estimation
• Tracking microspheres on cilia cells (master thesis)
• Air drag measuring from videos of falling objects (uni project)
• Nuclear foci tracking in timely resoluted mosaic images and cell pedigree estimation (WIP)
• Huang rank order filter visualization (uni project, see below)
• Softmax classifier visualization (uni project, see below)

Documentation

There are four types of documentation:

1. Code: The documentation of the code is done on this webpage. Just navigate with the panels on the left and on the top or use the serach function.
2. Manuals: There are user manual PDFs for each modul of the program. They are not public yet. Please contact me for more information.
3. Theory: My bachelor thesis about the concepts of ImageD and my master thesis about microsphere tracking on cilia in videos. Both not published yet. Please contact me for more information.
4. Tutorials: YouTube "how to" videos. See next section for direct links.

Weblinks

Some YouTube-Tutorials can be found here:

• Huang rank order filtering explanantion and visualization (german)
• kNN classifier (german)
• Softmax classifier (german)
• Selfmade watershed transform implementation (german)
• How diescrete fourier transformation works (german)
• Michelson interferometer simulation (german)

Projects

ImageD is used mainly in the field of biophysics at GSI Darmstadt.

List of projects, where ImageD was used:

• Estimating DNA fiber thickness: Correlative Light and Electron Microscopy (CLEM) Analysis of Nuclear Reorganization Induced by Clustered DNA Damage Upon Charged Particle Irradiation
• Quantification of immune cells in tumor slices: Reduction of lung metastases in a mouse osteosarcoma model treated with carbon ions and immune checkpoint inhibitors
• More projects will be added soon. Permissions needed to publish links here.

Third Party Software

To develop, document and distribute ImageD these tools where used:

• The main programming language is C++
• As IDE Qt Creator is used
• For the graphical user interface and some usefull classes the Qt Framework is used
• The base image container and some image processing methods come from OpenCV
• This documentation is created by doxygen
• The distribution and website hosting is done by git hub and git hub pages

Other

Thanks

Special thanks goes to:

• My former supervisor at GSI Dr. Michael Scholz who gives me a lot of freedom in developing ImageD and who trusts my skills
• The professors in Machine Vision and Photonics at Hochschule Darmstadt who always take time for my crazy questions. In particular Prof. Dr. Joachim Ohser, Prof. Dr. Thomas Netzsch and Prof. Dr. Christoph Heckenkamp
• My fellow students Chiara, Christian and Simon who are always good discussion partners with clever ideas

Developer

Information about the developer:

• Name: David Eilenstein
• Contact: D.Eil.nosp@m.enst.nosp@m.ein@g.nosp@m.si.d.nosp@m.e
• Degree: Bachelor and Master of Science in Machine Vision and Photonics at Hochschule Darmstadt
• Job: Writing ImageD and plugins for specialized solutions in the biophysics department at GSI Darmstadt
• Other: The species of athletic nerds actually exist :-P