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

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General information

Course name Blockveranstaltung: Introduction to image processing in biology with ImageJ and FIJI - online course
Subtitle
Course number 340066
Semester WiSe 2023/24
Current number of participants 21
maximum number of participants 15
notwendige Teilnehmeranzahl 5
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, 01.11.2023 09:00 - 16:00
Type/Form

Rooms and times

No room preference
Wednesday, 01.11.2023 09:00 - 16:00
Thursday, 02.11.2023 09:00 - 16:00
Friday, 03.11.2023 09:00 - 16:00

Fields of study

Comment/Description

An ever-increasing number of biological events can be recorded by means of micro- or nanoscopy. The resulting image-based data can be visualized and quantified with a growing array of open source software. A well-designed experiment may yield spatiotemporal information regarding events taking place at the organismal, cellular or molecular level. A proper evaluation thereof requires understanding of what an image is, how it was generated and what subsequent processing methods may be 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 underlying motivation for the course is the visualization and quantification of biological events based on microscope-generated images. The freely available "ImageJ"(< https://imagej.nih.gov/ij/ >) software package and its "FIJI" variant ([https://fiji.sc][1]) 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 images. Obtaining help from emerging technologies such as large language models will be discussed in this context. Other open source alternatives, such as "Cell Profiler" ([https://cellprofiler.org/][2]) or "ilastik" ([https://ilastik.org/][3]) will be introduced briefly.

Students attending the course may in advance 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.

The course will take place online and will be hosted by the City Campus Light Microscopy Facility (MPI MNAT); online participation information will be sent to participants 1 week prior to the course.

The course will last ~6 h/day.


Important:

Once participation has become binding after the signing-out period, cancellation is only possible via the GGNB or GAUSS Office with a) sick certificate, or b) statement by supervisor for scientific reasons. If you do not provide this, you will be excluded from courses for the next 12 months, as well as travel grants and other financial support. No exceptions.

By signing up you agree (1) to carefully check whether you will be able to attend the course (do not register for 2 courses taking place on the same dates - the above mentioned sanctions apply!), (2) to frequently check your student e-mail account, as all information on courses will exclusively be sent to that account; (3) that your name and e-mail address may be forwarded to the course instructor(s) for communication before and after the course; (4) to complete the course evaluation; (5) inform us if you no longer wish to maintain a waiting list position.

[1]: http://fiji.sc
[2]: http://cellprofiler.org/
[3]: http://ilastik.org/

Admission settings

The course is part of admission "GGNB_Methods_2023_WiSe_August_Oktober".
You can register and sign out for methods courses in October 2023 from 1-20 August 2023. The slots will be assigned around 25 August 2023.
In exceptional circumstances, you can still sign out until 31 August 2023.
Your participation becomes binding on 1 September 2023. Thereafter, cancellation is only possible via the GGNB Office with a) sick certificate, or b) statement by supervisor (for scientific reasons). If you do not provide this, you will be excluded from courses for the next 12 months, as well as travel grants and other financial support.

By signing up you agree (1) to carefully check whether you will be able to attend the course (do not register for 2 courses taking place on the same dates – the above mentioned sanctions apply!), (2) to frequently check your student e-mail account, as all information on courses will exclusively be sent to that account; (3) that your name and e-mail address may be forwarded to the course instructor(s) for communication before and after the course; (4) to complete the course evaluation.
The following rules apply for the admission:
  • The enrolment is possible from 01.08.2023, 00:00 to 20.08.2023, 23:59.
  • Enrolment is allowed for up to 2 courses of the admission set.
  • At least one of these conditions must be fulfilled for enrolment:
    • Degree is Promotion m.Abschlussprfg
    • Degree is PromStudiengang Cotutelle
    • Degree is Promotion Cotutelle
    • Degree is Promotionsstudiengang
    • Degree is Promotionsprogramm
    • Degree is PromProgramm Cotutelle
  • A defined number of seats will be assigned to these courses.
    The seats in the affected courses have been assigned at 25.08.2023 on 23:59. Additional seats may be available via a wait list.
  • At least one of these conditions must be fulfilled for enrolment:
    • Subject is Neurowissenschaften
    • Subject is Physik
    • Subject is IRTG 2172 - PRoTECT
    • Subject is Psychologie
    • Subject is Genes in Development, Disease and Evolution
    • Subject is Mathematical Sciences
    • Subject is PhysicsBiologComplexSyste
    • Subject is Cardiovascular Science
    • Subject is Molekulare Medizin
    • Subject is Biologische Diversität und Ökologie
    • Subject is Geoscience
    • Subject is Emerging Infect. Diseases
    • Subject is Geography
    • Subject is Computer Science -PCS-
    • Subject is Biologie
    • Subject is Catalysis Sust.Synt.CaSuS
    • Subject is SensoryMotor Neuroscience
    • Subject is BioNutz-MolwissBiotechnol
    • Subject is Umweltinformatik
    • Subject is Biomol:Struc-Func-Dynamic
    • Subject is Geographie
    • Subject is Systems Neuroscience
    • Subject is Behavior and Cognition
    • Subject is Genome Science
    • Subject is Theoret Computat Neurosci
    • Subject is Environmental Informatics
    • Subject is Materialforschung Holz
    • Subject is Molekulare Biologie
    • Subject is MolecularBiology of Cells
    • Subject is MetalSites i.Biomolecules
    • Subject is Environmental Informatics
    • Subject is MolecularPhysi oftheBrain
    • Subject is Chemie
    • Subject is Microbiology-Biochemistry
Assignment of courses:

Registration mode

The enrolment is binding, participants cannot unsubscribe themselves.