This Indico installation shall not be used to organise MPI-CBG courses and events from beginning of 2024 on. Please use MPG Indico instead.
19-21 February 2018
Center of Systems Biology Dresden
Europe/Berlin timezone

Registration deadline: 31 January 2018

Course aim:

Introduces novice users to basic concepts and techniques in quantitative image analysis.  Major topics covered include the basics of filtering and segmenting images along with techniques to extract useful measures from bio image data. Participants will learn how to use the Fiji software package and perform realistic bio-image analysis through numerous exercises and interactive hands-on sessions

Lerning Outcome:

By the end of the course participants will be familiar with:

  • Tools to open, explore (and reconstruct) multidimensional image data.
  • Tools to perform manual and automated segmentation and measurements in 2d and 3D images: segmentation (threshold, watershed) skeletonization, maxima detection, denoising filter and binary filters.
  • Time sequence analysis and object tracking (in 2D and 3D with trakmate and/or MaMut).
  • Good practices to report measures and perform repeatable analysis, as well as tips and tricks for bio image analysis.

The number of participants is limited to 12. Preference is given to DIPP PhD students

We will inform you after 31 January 2018 whether a slot in the course could be assigned to you!

Starts
Ends
Europe/Berlin
Center of Systems Biology Dresden
SR 1, ground floor
Pfotenhauerstr. 108 01307 Dresden

LECTURER: Benoit Lombardot MPI-CBG Scientific Computing Facility

COURSE STRUCTURE: Each part of the course contains some theoretical presentations, short exercises to apply new knowledge and a long exercise to start combining the tools and tackle more real life analysis.

Day 1

9:00 – 10:00: Image Characteristics and visualization

10:00 - 12:00: Region of interest and Measures

13:30 - 17:00: Automatic segmentation, the standard pipeline

Day 2

9:00 – 12:00: Measures in time sequence and tracking

13:30 – 17:00: Automatic segmentation, point line and scales

Day 3

9:00 – 11:00: Tools to visualize and explore N-dimensional data

11:00 – 12:00: Projects discussion

13:30 - 16:30: Segmentation in 3D images

16:30 – 17:00: Feedback round

Background Reading: https://imagej.net/Welcome

PREPARATION

Get your laptop ready for the course. You will need it to perform all the hands-on sessions and exercises. Before the course: Install a fresh version of Fiji on your laptop Download materials (link coming soon) Contact us if you have any issue with one of the above On the day of the course bring your laptop and power cable !

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