Blockveranstaltung: Introduction to image processing in biology with ImageJ and FIJI - online course - Details

Blockveranstaltung: Introduction to image processing in biology with ImageJ and FIJI - online course - Details

Close message box
You are not logged into Stud.IP.

General information

Course name Blockveranstaltung: Introduction to image processing in biology with ImageJ and FIJI - online course
Subtitle
Course number 340066
Semester SoSe 2020
Current number of participants 8
maximum number of participants 15
Home institute Göttinger Graduiertenzentrum für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB)
participating institutes Georg-August University School of Science (GAUSS) (für Mathematik und Naturwissenschaften)
Courses type Blockveranstaltung in category Teaching
First date Wednesday, 13.05.2020 09:00 - 23:59
Type/Form
Participants Target group: GGNB and GAUSS doctoral students.
Learning organisation The course will take place online, the link will be provided by course instructor Mišo Mitkovski: <mitkovski@em.mpg.de>
ECTS points 1.5

Rooms and times

No room preference
Wednesday, 13.05.2020 09:00 - 23:59
Thursday, 14.05.2020 09:00 - 23:59
Friday, 15.05.2020 09:00 - 23:59

Comment/Description

The course will last 7-8 h/day.


An ever-increasing amount of biological events can be acquired by means of micro- or nanoscopy and quantified with a growing array of open source software. A well-designed experiment may yield spatiotemporal information regarding events taking place at the cellular or molecular level. A proper evaluation thereof requires understanding of what an image is, how it is generated and what subsequent processing methods are available. A major aim of the course is to make participants aware of resources they can use to educate themselves toward successful experimental design, image acquisition and analysis.

The main underlying motivation for the course is the quantification of biological events through analysis of images generated with a microscope. The freely available "ImageJ" (<http://rsbweb.nih.gov/ij/>) and its "FIJI" variant (<http://fiji.sc>) are some of the several open-source applications that will be introduced towards this goal. First, the components of an image will be discussed, as well as the frequently used image types within their appropriate context. Basic concepts such as lookup tables, image calibration or the creation of multi-channel (overlay) images will be explained along with several standard situations that a microscope user is faced with on the road toward publication. Examples of basic image arithmetic and further image processing related to image stacks (i.e. time series) and 3D reconstruction will be introduced. More advanced topics will include the modification of ImageJ installs to suit the respective need. A third of the course will be dedicated to the ImageJ macro/programming language with the goal to automatically process and quantify a large amount of images. Other open source alternatives, such as "Cell Profiler" (<http://cellprofiler.org/>) or "ilastik" (<http://ilastik.org/>) will be introduced briefly.

Students attending the course may suggest related topics they wish to have covered.  IMPORTANT: The course aims to give students without experience in image processing a way to enter the field.

Admission settings

The course is part of admission "GGNB_Methods_2020_SoSe_February_April".
You can register and sign out for courses in April from 1-20 February. The slots will be assigned around 25 February.
In exceptional circumstances, you can still sign out before 29 February.
Your participation becomes binding on 1 March. Thereafter, cancellation is only possible with a) sick certificate, or b) statement by supervisor. If you do not provide this, you will be banned from courses for the current and next semester, as well as travel grants and other financial support.
By signing up you agree to frequently check your student e-mail account, as all information on courses will exclusively be sent to that account.
The following rules apply for the admission:
  • At least one of these conditions must be fulfilled for enrolment:
    • Degree is Promotionsprogramm
    • Degree is Promotionsstudiengang
    • Degree is PromProgramm Cotutelle
    • Degree is Promotion m.Abschlussprfg
  • The enrolment is possible from 01.02.2020, 00:00 to 20.02.2020, 23:59.
  • At least one of these conditions must be fulfilled for enrolment:
    • Field of study is PhysicsBiologComplexSyste
    • Field of study is Geography
    • Field of study is Mathematical Sciences
    • Field of study is Geographie
    • Field of study is Environmental Informatics
    • Field of study is Biomol:Struc-Func-Dynamic
    • Field of study is Chemie
    • Field of study is Emerging Infect. Diseases
    • Field of study is Microbiology-Biochemistry
    • Field of study is Geoscience
    • Field of study is Molekulare Biologie
    • Field of study is Environmental Informatics
    • Field of study is Behavior and Cognition
    • Field of study is Biologische Diversität und Ökologie
    • Field of study is Genome Science
    • Field of study is Theoret Computat Neurosci
    • Field of study is Genes in Development, Disease and Evolution
    • Field of study is Catalysis Sust.Synt.CaSuS
    • Field of study is Neurowissenschaften
    • Field of study is IRTG 2172 - PRoTECT
    • Field of study is Physik
    • Field of study is Umweltinformatik
    • Field of study is Molekulare Medizin
    • Field of study is Systems Neuroscience
    • Field of study is MolecularBiology of Cells
    • Field of study is MetalSites i.Biomolecules
    • Field of study is Computer Science -PCS-
    • Field of study is SensoryMotor Neuroscience
    • Field of study is BioNutz-MolwissBiotechnol
    • Field of study is Materialforschung Holz
    • Field of study is Biologie
    • Field of study is MolecularPhysi oftheBrain
  • A defined number of seats will be assigned to these courses.
    The seats in the affected courses have been assigned at 29.02.2020 on 23:59. Additional seats may be available via a waiting list.
  • Enrolment is allowed for up to 2 courses of the admission set.
Assignment of courses:

Registration mode

The enrolment is binding, participants cannot unsubscribe themselves.