Image Analysis

The Bio-Imaging Facility provides several high-end analysis workstations equipped with state-of-the-art image analysis software. In addition, we provide project based solutions for custom-tailored image analysis tasks: we help you to automate your image analysis workflow, or establish new image analysis routines using the image analysis programs available at I.S.T. Austria*.

• Image analysis software
• Image analysis tools
• Image analysis workstations
• Booking policy
• Data storage policy

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Community resources:

Reading tips:

• Guidelines for Best Practices in Image Processing
• Lossy Compression Degrades Data → Online Learning Tool for Research Integrity & Image Processing
• NIH Image to ImageJ: 25 years of image analysis → Nature Methods
• Fiji: an open-source platform for biological-image analysis → Nature Methods
• ImageJ Online Guide
• iBiology image analysis seminar by Kurt Thorn (2012)

Courses and network:

• Open image analysis forum: https://forum.image.sc → for all your image analysis questions
• Bio-Image Analysis Network (BIAS): http://eubias.org/NEUBIAS/  → for conferences and workshops!

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Freeware:

• • • FIJI*: https://fiji.sc/ → Fiji is an image processing package – a “batteries-included” distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis
    • ICY: http://icy.bioimageanalysis.org/ → an open community platform for bioimage informatics
    • Ilastik*: https://www.ilastik.org/ → a simple, user-friendly tool for interactive image classification, segmentation and analysis
    • BisQue: https://bioimage.ucsb.edu/bisque →  Store, visualize, organize and analyze images in the cloud
    • Cell Profiler:https://cellprofiler.org/ → Load; Adjust; Process; Export; Explore your images and data
    • KNIME: https://www.knime.com/knime-for-data-scientists →  plug-and-play different image analysis tools together in a connection node-based workflow scheduler
    • GNU Octave: https://www.gnu.org/software/octave/ →  a high-level language, primarily intended for numerical computation
    • bioimagexd: http://www.bioimagexd.net/ →  analyzing, processing and visualizing multi-dimensional microscopy images
    • plant image analysis web: http://www.plant-image-analysis.org/ →  a database of image analysis tools, plug-ins and programs, mostly designed specifically for plant-related research

Commercial Free:

• • • Leica: LAS X Core-Lite*
    • Nikon:  NIS free viewer*
    • Olympus: OlyVia 2.9 viewer* (slidescanner)
    • Zeiss: Zen Lite*

Commercial:

• • • Arrivis Vision 4D*: https://www.arivis.com/
    • Bitplane Imaris*: http://www.bitplane.com/
    • Mathworks Matlab*: https://www.mathworks.com/
    • Imspector (dongle)*
    • SVI Huygen*: https://svi.nl/HomePage
    • Zeiss Zen 2.3-5*: https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html
    • Nikon NIS-Elements + Jobs*: http://www.nis-elements.cz/en/solutions/jobs/27