High Performance Image Analysis Computer

The NCBC has a high performance Windows 10 workstation for analysis of large imaging datasets. The computer has an installation of Bitplane Imaris as well as Matlab, Python, Fiji, and Leica LAS X Core Offline. The workstation "specs" are:

  • CPU: Dual 3.2 GHz 8-Core Xeon, 25 MB cache
  • RAM: 512 GB
  • GPU: NVIDIA Quadro P6000 24 GB
  • Storage: 4 x 1 TB SSD RAID 0

Bitplane Imaris

Imaris is image analysis software developed by Bitplane that is specialized for rendering and analyzing multidimensional datasets, including those acquired on our lightsheet and confocal microscopes. It has a variety of sophisticated algorithms for measuring and quantifying co-localization of fluorophores in 3D; performing automated, semi-automated, or manual segmentation of cell structure (including neural processes); and rendering animations of complex imaging datasets. 

The NCBC currently has the following Imaris modules available for use: Imaris Stitcher, Imaris FilamentTracer, and ImarisColoc (colocalization). Imaris Stitcher allows for the precise and accurate stitching of multiple image tiles in XYZ. Imaris FilamentTracer can be used to automatically detect neurons and other filament-like structures in 2D, 3D, and 4D. ImarisColoc allows the user to quantify and document co-distribution of multiple stained biological components. 

See Imaris, Imaris Stitcher, Imaris FilamentTracer, and ImarisColoc to learn more.

Behavior Video Analysis Workstation

The NCBC also has a Windows 10 workstation for video analysis of behavioral data using Ethovision XT or Freezescan software. 

Ethovision XT

Ethovision is a software program developed by Noldus you can use to perform experiments where the tracking of the mouse's location and/or behavior is necessary. It can be used with "live" or prerecorded video to measure the behavior, movement, and/or activity of any animal. The user defines the task parameters, defines the task arena and designates any focal areas, sets up the use of any accessories (i.e. optogenetics), and sets the detection parameters for tracking the subject mice. As such, it is an ideal program to use in tasks where the measurements of interest include: frequency of behavior, time spent in a set location, orientation towards, etc. Ethovision can also be used in optogenetics experiments (or others), allowing users to set the onset of the laser to occur when a certain behavior/movement/mouse location is detected. 

Learn more by visiting the official Ethovision site.


FreezeScan is a software program developed by CleverSys that can automatically detect freezing in Fear (Threat) Conditioning experiments. It can be used with "live" or prerecorded video and eliminates the possible confounds that arise from manual scoring. The user defines the task parameters as well as the arena that is to be tracked for mouse freezing. Learn more by visiting the official FreezeScan site.