27 Jan, 2020 @ 9:30 am – 31 Jan, 2020 @ 5:00 pm
In this course, you will learn how to analyze the movement and behavior of invertebrates from videos. The aim is to offer you a new analytical tool to study the causes and consequences of movement in small organisms, ranging from insects to zooplankton. The course will cover all the salient aspects of video analysis, starting with basic and advanced video filming techniques (data acquisition), experimental design, and analytical pipelines for testing movement and behavior under different environmental conditions, and at population and community level. Original data will be collected and analyzed, plus a published dataset (DOI:10.4228/ZALF.DK.92) will be explored during the course.
After the course, the attendee will be able to acquire and manipulate video files under a solid, automatic analytical workflow, to modify and create custom ImageJ macros, to run two different auto-tracking routines and to explore and analyse movement data (Type II trajectories).
Basic experience with R is required to attend the course.
- filming techniques and video setup
- experimental design
- automatic trajectory extraction with R and ImageJ
- data cleaning and visualization (gganimate)
- statistical methods of movement analysis
Tracking particles in video data:
- Observing behavior in small organisms
- Filming techniques
- The camera (shutter, diaphragm, ISO speed)
- Introduction to R, ImageJ & ffmpeg
- Introduction to video file formats and databases
- Movement and morphology descriptors
- Capturing moving particles in manual tracking (TrackMate)
Editing video files:
- ImageJ basics
- Particle analysis
- Binary video operations
- Batch analysis
- Macro scripting
- Video enhancement, size compression
Introduction to BEMOVI (R package):
- Video files batch conversion
- Folder structure and data input/output
- The BEMOVI pipeline
- Error filtering – trajectory clean-up
Introduction to TrackDem (R package) :
- Particles simulations
- The TrackDem pipeline
- Error filtering with neural networks
- From arrays to dataframes
From code to interpretation:
- Statistics for movement data
- Movement parameters (speed, turning angles…)
- HMM models (state-space models)
- Fit a distribution
- Static vs. dynamic graphics
- Basic and advanced trajectories visualization
- Base R and ggplot
- Graph animation (gganimate)
- GIF output for data presentation
Trajectories of Daphnia magna under visible light (left) and UVA radiation (right). Colangeli et al. 2016.
Pennekamp et al. 2015. “BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes.” Ecology and Evolution
Colangeli et al. 2018. “Negative phototactic response to UVR in three cosmopolitan rotifers: a video analysis approach.” Hydrobiologia
Colangeli Pierluigi, Ph.D.
Hyblea Training, Italy
Topics: plankton ecology, movement and behavior analysis, biodiversity
EARLY-BIRDS DEADLINE: 15 OCT 2019
REGISTRATION DEADLINE: 15 DEC 2019
Up to 30 days before the beginning of the course: complete ticket price refund (minus billing operations, depending on the payment method).
Less than 30 days before the beginning of the course: no refund available.
HT is not refunding travel and accomodation costs.