Image analysis & processing services

The LS&E microscopy and Image analysis core facility center provides bio-imaging and bio-analyst services such as developing image processing and analysis workflows, writing macros for automation of image segmentation, and analysis protocols by using state of the art image analysis tools and software like FIJI, Image J, CellProfiler, Ilastik, Imaris, etc’.

 

HIVE server – Central Data Hub

Storage Module:   
Data expansion bus for 56 TB neto (RAID6) storage.
Increases disk write speed to ~900 MByte/sec
Storage volume of 148 TB (2 modules)

Computation Module:
3.9 GHz HEX core CPU
10 GBit/sec network uplink.
15 TB comution volume in RAID5 configuration for data safety.
256GB RAM

 

 

 

 

 

 

HIVE server a platform for image processing and visualization

Designed for processing
For image based microscopy datasets (widefield, confocal, SPIM, etc.)
For processing using Open Source and Commercial image processing software (ImageJ, Fiji, Ilastik ,IMARIS, MatLab and others)
For batch deconvolution of large multidimensional datasets (Huygens Professional, ZEN and etc.)

Designed for visualization
For multidimensional data using Open Source (FIJI), and Commercial volume rendering software (IMARIS)|

 

• • Imaris – 3D/4D/5D Image analysis software, an ideal software for viewing, rendering and measurements of 3D and 4D (3D+time) data sets, including 3D colocalization, 2D and 3D tracking and more
  • ZEN – Image analysis and Airyscan & Elyra image processing software from Zeiss
  • QuPath – Histology section visualization and analysis software (freeware)
  • ImageJ/Fiji – image analysis (freeware)
  • Gen5 – Image analysis software for Cytation 5 microscope from Agilent
  • Cellprofiler – Cell image analysis software for high-content image data (freeware)
  • ilastik – An interactive learning and segmentation toolkit (freeware)
  • MorphoGaraphx – open source application for the visualization and analysis of 4D biological datasets.