Equipment: Hardware and Software

State of the Art Computing Hardware for Image Analysis

Lightsheet microscopy requires a large investment in computational capabilities. Our lab is equipped with everything you will need to handle the largest of images with ease. We use server grade hardware to remove the technical obstacles from working with lightsheet microscopy. 

Our workstations use dual Xeon server processors, a minimum of 300Gb of RAM, 16Gb-24Gb of dedicated video RAM, fast onboard storage and access to our 10Gb network. 

Additionally, we store all your files on our extremely fast network attached storage (NAS) with over 250Tb of redundant storage space. Access your files anytime through the campus network (10Gb only in Light Hall) and always retain control over your data.

SmartAnalytics Software

LifeCanvas Technologies’ SmartAnalytics software is a graphical interface-based tool for performing quantitative analysis on 3D fluorescent microscopy image data collected with the SmartSPIM microscope.

The standard workflow consists of 3d image registration to a defined atlas (e.g. the Allen Mouse Brain Atlas) and execution of whole volume cell detection using provided machine-learning models or measurement of fluorescent signal. Results are summarized per atlas region with a variety of output format and visualization options.

Detection Models Include:

  • Neurological disease markers
    Cell detection models for GFAP, IBA1, β-amyloid, and α-synuclein Lewy Bodies provide a detailed measure of disease progression and expression in a mouse brain. 

  • Neural activity
    Detection of cFOS+ cells in a whole mouse brain gives insight into brain activity levels that is unaffected by region selection bias. 

  • Cell type markers
    SmartAnalytics software identifies and quantifies many types of cells, including neurons labeled with TH, PV, NeuN, endogenous fluorescence such as GFP, and more. 

  • See how it works here

Innovative 3D Neuron Tracing with Imaris

The Imaris for Neuroscientists package is the perfect combination of tools for researchers working in various neuroscience disciplines.

Imaris enriches advanced 3D/4D visualization and analysis methods with Filament Tracer — best in class software for an automated detection of neurons including spines and other filamentous structures in 2D/3D or 4D datasets, measurements, object tracking, plotting, group comparisons with statistical tests and two-way interface for customization in Matlab, Java or Python.

Imaris provides a complete set of features for visualization of multi-channel microscopy datasets from static 2D images to 3D time series regardless of their size and format.

Using Imaris for Neuroscientists users can:

  • Organize and manage full experiments including images and data analysis in Imaris Arena.

  • Use premier 3D/4D volume rendering modes: (MIP, Blend Projection, Shadow Rendering, Normal Shading)

  • Benefit from Imaris high performance IMS file format which guarantees smooth navigation even in very large 3D datasets (TB range)

  • Combine volume rendering, object representation, clipping planes and cross-section slices

  • Make high quality snapshots ready to be used in publications in Snapshot Tool

  • Easily make animations which include volume rendering, detected objects, annotations, object motion by adding several frames of interest in a Key Frame Animation Tool

VNL users have access to this software suite installed on a graphics workstation with dual 46-Core Xeon Processors, 512Gb of RAM and an NVIDIA QUATRO card with 24Gb of video ram.

Scientific Data in Virtual Reality

syGlass software allows you to view your data in its actual 3D or 4D (over time) form through virtual reality. syGlass allows you to explore very large data sets that are generated by microscopes, patient, and industrial scanners.

Use our tools to quantify your data with enhanced precision, or import your results for rapid correction in VR. Our mission is to provide tools for investigators to understand complex data sets completely and communicate their findings efficiently.

Launched by an NIH Innovation Grant, syGlass grew out of neuroscience and computer vision laboratories at West Virginia University. syGlass was initially designed for the university’s neuroscience researchers, overcoming a major problem they faced: complex and large datasets viewing neurons and their connections across scales of resolution. Inundated with requests by other scientists to use our software, we worked to affordably commercialize syGlass and share our inventive features for laboratories around the world.

Super fast quantification in 3D:

  • Automatically count cells and other objects, then quickly correct any errors

  • Count, trace, measure, segment, and track objects through time with perfect accuracy

  • Track structures through time and space in 4D

  • See true and false positives easily with stereoscopic vision

VNL users have access to syGlass software running on our high-end graphics workstations. We use HP Reverb 2 virtual reality headsets for single or collaborative meetings in virtual space. View your large data sets with your collaborators in a way you have never seen before. Gain new insights. Make discoveries.