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Image Processing and Visualisation with LithoGraphX

LithoGraphX

Description

LithoGraphX is a software to visualize, process and analyse 3D images and meshes.

On the first day of this course, we will demonstrate how to use LithoGraphX to visualize, clean and process 2D and 3D images. We will cover: (i) how to extract cell shape from 2D or 3D images by marking the cell wall or membrane, (ii) how to extract key morphological features and (iii) how to use these features to build a cell classifier. The first day is intended for biologists and computer scientists interested in using LithoGraphX.

On the second day, we will see how to write and distribute extensions to LithoGraphX. To this purpose, we will learn more about the internals of LithoGraphX and its API both in C++ and Python. The second day is intended for computer scientists wanting either to write their own algorithm or automate complex protocols.

Participants can choose to register for both days or for individual days, depending on their interest and background knowledge.

 

Trainers

Pierre Barbier de Reuille, University of Bern

 

Audience and Prerequisites

  • Day1 is intended for biologists and computer scientists interested in using LithoGraphX. Some experience in imaging is desirable but not required.
  • Day2 is intended for computer scientists wanting either to write their own algorithm or automate complex protocols. Basic python knowledge and familiar with C++ are required.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals

 

Syllabus, Tools and Resources

During this course you will learn about:

  • Software: LithoGraphX and FiJi
  • Methods: image visualization, preprocessing and segmentation, feature extraction, basic machine learning
  • Development: internal data structures of LithoGraphX, plugins and packages in C++ and Python

 

Learning Objectives

After this course you should be able to:

  • Use the LithoGraphX user interface and find help
  • Perform automated and manual cleaning, preprocessing and 2/3D segmentation using LithoGraphX
  • Build and use a cell classifier with LithoGraphX
  • Write a process in LithoGraphX
  • Prepare and compile a source package as well as prepare a binary package

 

Links

Book Here

 

Timetable

Time

Subject

Day 1

10:00

Principles of LithoGraphX

11:00

Loading an image and tuning the visualization

12:00

Lunch

13:00

Preprocessing and segmentation of 3D cells

14:00

Preprocessing and segmentation of 2D cells from 3D images

15:00

Segmenting 2D images and machine learning

16:00

Basic automation using Python scripts

 Tea/coffee provided in between sessions

Day 2

10:00

Processes, plugins and packages: how to extend LithoGraphX

11:00

Extending LithoGraphX in python: writing and distributing processes

12:00

Lunch

13:00

Packages: source vs binary. How to compile and distribute packages.

14:00

Plugins: management and resolution of conflict.

16:00

How to write C++ processes and internal structures of LithoGraphX

 Tea/coffee provided in between sessions

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