Image analysis & processing

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’.


image analysis tools

HIVE server – Central Data Hub

Storage Module:    HIVE server
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.







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
  • InCell Investigator – High Content Analysis software. This software is doing rapid, automatic segmentations and measurements for massive amount of data sets, thus doing high content analysis of images
  • InCell translator – translate image formats so that they can be analyzed by the InCell investigator
  • AxioVision measurements – measurements pro and auto measurements
  • Full LSM and Full ZEN for confocal imaging processing and analysis
  • Spotfire – software for a highly visual and interactive environment for exploring data
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