HHU StartMedizinische FakultätmedRSDVeranstaltungen / KurseScientific Image Processing and Analysis

Scientific Image Processing and Analysis

medRSD Workshop

Zielgruppe

Promovierende der Medizin (medRSD Mitglieder)

Promovierende der Naturwissenschaften (iGRAD Mitglieder)

 

Betreuer und Postdocs
Wissenschaftliche Mitarbeiter des UKD

SpracheEnglisch
Workshopdauer    2-tägig
Kursplätze15
Kursgebühren450 € für externe Teilnehmer, für Doktoranden und wissenschaftliche Beschäftigte der Med. Fakultät der HHU ist die Teilnahme kostenlos.
Anmeldung

medRSD: Anmeldung siehe unten

iGRAD: Anmeldung über das undefinediGRAD-Office

AnrechnungIm Ausbildungsprogramm der medRSD:
2 Veranstaltungstage im Bereich Kernkompetenzen
Im Basiscurriculum des PhD-Programms:
2 Veranstaltungstage im Bereich Wissen & Wissenschaft

Termine

Online-Kurs: MRS 225.20 Scientific Image Processing and Analysis
Termin: 28.09.2020, 29.09.2020, 30.09.2020
Uhrzeit: 09:00 - 15:00 Uhr
ANMELDEN

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Wir bitten Sie um eine Rückmeldung, falls die Termine in der Bestätigungsemail von den Angaben auf der Homepage abweichen.

Workshop Description
The workshop – “Scientific Image Processing and Analysis” aims to teach natural scientists from different areas of life science how to handle and process digital images starting from microscopic image acquisition on until the incorporation into the final publication figure. This includes important theory about high quality digital images in general as well as a broad spectrum of methods for correct image processing and specific analytical purposes according to high scientific standards. You will learn how to extract most information from your images and how to quantify regions of interest. Additionally, the workshop includes a lot of hands-on sessions and explains how to save time during repetitive image processing steps You will be able to revisit the learned material using the provided exercises and script also later on. The workshop content is generally of importance for scientists working with digital images and their analysis.

Specific Topics (among others)

  • Basics about correct image acquisition

    • Image formats - which formats serve scientific images and which should be avoided
    • Metadata - information saved beyond the visible image
    • Information content of images - learn about bit-depth, color spaces and different image types (or: how much information can be saved in and retrieved from an image).

  • Correct image adjustments avoiding alterations - contrast and brightness, image rotation, size changes, background subtraction methods.
  • Use of different image filters to improve extractability and preparation for further analysis
  • Image segmentation - How to extract specific objects of interest (e.g. cells positive for a certain marker stain)
  • Automated object counting
  • Image Quantifications (selected topics depending on participants field of interest):

    • Measurements of areas, area fractions, shapes, intensities…)

  • Dimension scaling of images
  • Labeling of (scale bars, calibration bars,…)
  • Ethics in image handling, processing and publication - where are the limits?!
  • Process automation using macro recording and batch processing.

Aim
The workshop should give scientists a better understanding about the Do's and Don'ts during digital image processing and insight in the methodology of extracting a multiplicity of information from their images. The participants will gain extensive knowledge about the possibilities they have to analyze their imaging data.

Target Group
PhD Students and PostDocs working or planning to work with digital images. The workshop has a focus on microscopic images but all the content is applicable for digital images of different origin in general. No previous software knowledge required, but of advantage.

Methodology
During the practical parts of the workshop we will use the professional software Fiji (customized ImageJ bundle). The software is free and installation instructions will be given in advance.


Trainer
Dr. rer. nat. Jan Brocher (www.biovoxxel.de)

Requirements for participation in the online course
The workshop will be held online with a video conferencing system. The following requirements are necessary:
 
Hardware:
- Macbook/Mac or PC/Notebook
- A second monitor, or alternatively a second device (e.g. a tablet), or a connection to a TV set is recommended, as active participation on one's own computer is required parallel to the webinar!
- A camera is not absolutely necessary, but helps to improve communication.
- Microphone (the microphones available with the above mentioned devices are sufficient)
- The use of headphones is strongly recommended to reduce echo effects.
 
Software:
- Fiji (detailed instructions for installation and preparation will be sent to the registered participants by mail in time)
- Zoom will be used as a platform for the workshop and the video conference. It makes sense to install the Zoom App. It is NOT necessary to register with Zoom.
 
More detailed information and instructions, as well as the access data for the webinar will be sent to the participants by e-mail a few days before the workshop starts. Please also check your SPAM folder.

Verantwortlich für den Inhalt: E-Mail sendenDekanat der Medizinischen Fakultät der HHU