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Scientific Image Processing and Analysis

medRSD Workshop
Audience Doctoral researchers in medicine (members of medRSD)
Doctoral researchers in natural sciences (members of iGRAD)
Supervisors and Postdocs
Scientific researchers at the Faculty of Medicine at HHU
Language English
Duration 2 days
Capacity 15
Costs 450 € for external participants
Free for doctoral researchers and research associates at the Faculty of Medicine of HHU
Registration medRSD: See below how to register
iGRAD: Please contact iGRAD-Office

In the training programme of medRSD:
2 days - professional skills
In the Basic Curriculum of the PhD programme:
2 days - Science: Basics & Beyond

Dr. Jan Brocher
www.biovoxxel.de

The workshop will be conducted online using a video conferencing tool. The following is required:

Hardware:
- Macbook/Mac or PC/notebook.
- A second monitor, or alternatively a second device (e.g. a tablet), or a connection with a TV set is recommended, since parallel to the webinar you have to work actively on your own computer!
- A camera is not mandatory but contributes to better communication.
- Microphone (the microphones provided 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 emailed to registered participants well in advance of the course.)
- Zoom will be used as the platform for the workshop and the video conference. It is useful 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 workshop, will be emailed to participants a few days before the workshop starts. Please also check your SPAM folder.

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 or while building your publication figures in a way that preserves image quality and stores processing data. 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. Optional topics will be adjusted to meet the participants needs as good as possible if there is time left.
Furthermore, specific participant question regarding image processing or solutions for analysis issues can be personally discussed if communicated beforehand (e-mail with question and example images).

Specific Topics (among others)

  • Basics about correct image acquisition
    • How to achieve good image resolution (sampling)
    • 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 and tracking of moving objects (optional)
  • Basic 3D reconstructions (e.g. microscopic z-stacks, or medical MRI-Data)
  • Image Quantifications (selected topics depending on participants field of interest):
    • Measurements of areas, length, …
    • 3D object analysis (volume, surface, distances, angles…)
    • How to correctly measure intensities in images (e.g. fluorescence)
  • Dimension scaling and calibration of images
  • Labeling of images and time series/movies (text, numbers, scale bars, calibration bars,…)
  • Ethics in image handling, processing and publication - where are the limits?!
  • How to efficiently prepare publication figures.

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

Doctoral researchers 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.

Methodology

During the practical parts of the workshop we will use the professional software Fiji (customized ImageJ bundle). All necessary software will be provided (open source!).

Trainer

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

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