Veranstaltungsdaten

Beschreibung: 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; (6) that you only receive credits for attending the entire workshop - you will not get partial credits for part-time attendance.

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