CoRE Informatics

For intensive multidimensional image processing the Microscopy and Advanced Bioimaging CoRE houses:  An image analysis Server (Acquifer HIVE) with 512GB of RAM, 32 Processing Cores, and an Nvidia A6000 48GB GPU; A high-end workstation (2TB RAID0 NVMe-SSD, 128GB RAM, 2x 8-Core Xeon @2.6GHz, 16GB Nvidia Pascal VRAM); A RAID6 100TB upgradeable file server with top-of-the-line read/write speeds; A networking module which in combination with our 10Gbit local network allows extremely fast transfers and on-the-fly as well as offline analyses from imaging stations. In addition, the Core has two high-end workstations for 4D analysis and two mid-level workstations used for 2D/3D analysis and open-source pipeline development. Each microscope is equipped with a high-end workstation also capable of on-the-fly image processing. The High-Content Screener is connected to a server (90TB RAID5, 96GB RAM, 2x 4-Core Xeon @2.6GHz) that handles the SQL database and which can be used for other applications as well.  

Please consult with us for all image acquisition and analysis needs. 

Analysis Software

The Core has licenses and service agreements for cutting-edge image analysis software.  

4D Analysis

Bitplane Imaris
Arivis Vision4D  

Deconvolution

Autoquant X3
SVI Huygens
Leica Lightning

2D-3D Analysis   

ImageJ/ Fiji
MetaMorph
Volocity
QuPath  

Custom and open source: Custom analysis pipelines are developed on proprietary or open-source platforms  

ImageJ Scripts and Pipelines, including MicroManager
Cellprofiler
Ilastik
MATLAB routines
Python
R for statistical computing
Terastitcher
CLEARMap