Bioimaging Wiki

This workstation has Amira v2020 for 3D image processing and analysis and the Gen5 software (for processing+analysing Cytation5 datasets). It can also be booked for processing demanding FIJI, QuPath and Ilastik operations, and other open-source tools (eg, AI/ML workflows). If you are not familiar with Amira you can find excellent tutorials here: https://www.youtube.com/playlist?list=PLoxdPzacxPYjDVMD4tPCaVbuQjxYizr_g

CPU: Intel i9 9900X (10×2 cores) @3.5GHz (max 4.4GHz)

RAM: 128 GB DDR4

Graphics: nVidia GeForce RTX2070 - 8 GB VRAM

OS: Windows10 Pro 64 Bits

Data storage: 1TB SSD + 8Tb HHD (both temp space only!)

⇒ Data is automatically deleted after 3 months of inactivity!

• FIJI
  • FIJI is just ImageJ (“batteries-included” distribution of ImageJ2)

• QuPath 0.4.3
  • Open Software for Bioimage Analysis of whole slide images

• Zeiss ZEN Blue 3.3 Desk
  • Airyscan Processing, Stitching and MIP of .CZI files

• 3i Slidebook Reader 2022
  • Supports .SLD file format.

• Nikon NIS-Elements Viewer 5.21
  • Supports .ND2 file format

Data files older than 3 months will be automatically deleted on this system, please copy your data to the server using the desktop link.

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