Arivis Vision 4d
Modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited sizes independently of available RAM.
Installation: 1 x floating licence available on all workstations (book it as ‘equipment’ in addition to your workstation reservation!)
Fiji is an image processing package: a “batteries-included” distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
A simple, user-friendly tool for interactive image classification, segmentation and analysis.
- weblink: http://ilastik.org/
- installation: all workstations
Bitplane Imaris: 3/4D Image Visualization and Analysis Software
We have 8 x Imaris 9.3 floating licences available on all our workstations. The floating licences need to be booked in PPMS as separate resources:
- One View, a new Arena view that performs as a microscopy image browser mirroring your internal, external, and network drive file systems.
- One Pipeline, improved batch processing to include image processing functions. Perform those functions and your object wizard-based analysis within just one pipeline.
- Imaris file converter: (batch) convert (multiple) datasets to ‘.ims’ format. Imaris converter is integrated in imaris 9.3 or above.
- ClearView™ deconvolution (1x): this is an Imaris deconvolution licence: please only select this option in case you need it during your session, and don’t forget to deactivate it after your session! – please book as Special Environment 1 on the floating licence reservation in PPMS
- Imaris stitcher (1x): for stitching tiled image stacks – please book as Special Environment 2 on the floating licence reservation in PPMS
For your convenience, the usage of the Imaris licences can be seen here: http://login2.ist.local/current_imaris_users.html
- The log is updated automatically every 10 minutes
- In case you booked it and you cannot use it, this tool helps you to identify which user is using it without booking …
A desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly
- weblink: https://www.mathworks.com/products/matlab.html
- installation: campus-licence available on all workstations
Wolfram Research Mathematica
Technical computing environment for arbitrary precision arithmetic and symbolic computation.
- weblink: http://www.wolfram.com/mathematica/
- installation: Installed on Analysis workstation #8, using a campus floating licence.
- installation: workstation 3,4,5 and 6 – only 1 x dongle available (book it here)
Deconvolution: a mathematical operation used in Image Restoration to recover an image that is degraded by a physical process which can be described by the opposite operation, a convolution.
- weblink: https://svi.nl/HomePageSVI Huygens Deconvolution needs to be booked as separate resource in PPMS! There is no additional charge to this, but we want to make it clearer and for you to see the availability of our resources. We have 2 floating licences that can be booked here: SVI Huygens float 1& SVI Huygens float 2
Packages: Huygens Professional / Widefield & Brightfield / Confocal / Spinning Disc / STED-STAB / Array Detector (Airyscan & SPAD) Optical option / Full File-readers Option / Time option / Object Stabilizer / Deconvolution & Batch Express / Hot Pixel Remover / Twin-Slicer / Ortho-Slicer / MIP-Renderer / PSF Renderer / PSF distiller / Chromatic Aberration Corrector / Performance Option
Zeiss Zen 2.3
- lite versions on all workstations
- Zen 2.3 full version for stitching: workstations 2, 3, 4 and 5, additional Airyscan processing module on workstations 3 and 5
The leading platform for single-cell flow cytometry analysis that helps your research stand out.