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