The off-line image processing workstation is available for use within the outer room (Room 006, BBE) of the Carver Center for Imaging (CCI). The workstation complements the existing confocal and multiphoton imaging systems (Leica SP5, SP8, STELLARIS 8) within the CCI to enable high-end image processing and analysis. We have also upgraded networking infrastructure to provide fast transfer of data from the SP5, SP8, and STELLARIS 8 machines to the off-line workstation. The hardware and software were purchased with a grant from the Roy J. Carver Charitable Trust and supplemented by funds from the Department of Biology.
Hardware
We purchased a high-performance computer workstation (HPZ6G4 CUDA PC with Windows 10 Professional 64-bit operating system coupled with NVIDIA graphics card with advanced Pascal GPU architecture) and a large curved 37.5” monitor. We also upgraded the infrastructure (added 10 gigabit cabling and network cards) to enable rapid off-loading of large data sets from the SP5, SP8, and STELLARIS 8 microscope PCs to the workstation.
Software
To provide a breadth of image processing, analysis, and visualization options, we purchased two complementary software packages (Leica and Imaris). The Leica LAS-X 2D/3D software streamlines processing and analysis of image data collected by the Leica image capturing systems. Leica software also simplifies post-experiment deconvolution (Lightening) and 3D reconstruction. The Imaris 9.6 3D/4D Visualization & Analysis package adds sophisticated quantitation features, including the ability to track objects in three dimensions over time, to assess synaptic density, and to segment and quantify complex 3D structures such as neurons and glia, among many other applications. The following tables summarize the basic features of the Leica and Imaris image analysis modules.
| Module | Features |
|---|---|
| LAS X 2D Analysis | Workflow guides researchers step by step through 2D image analysis from applying filters, thresholding, and binary image processing to measurements, tracking, classification and reporting. |
| LAS X 2D Analysis Multi-Channel Extension | Samples with several acquisition channels can be analyzed in one run by assigning different analysis channels. The results can be used to correlate objects that are found in different acquisition channels. |
| LAS X 3D Visualization | Visualization tool for reconstruction and processing of 3D data |
| LAS X 3D Analysis | 3D analysis including interactive measurement, analysis wizard and processing toolbox |
| LAS X Lightning Process | Offline deconvolution and reconstruction software package for confocal, STED, and multiphoton data |
| Module | Features |
|---|---|
| Imaris Core | Render 3D/4D images, interactive visualization, snapshot & animation |
| MeasurementPro | Adds geometric and intensity measurement capabilities; detect structures for number, volume, intensity, size, shape & distance measurements (e.g., synapse colocalization) |
| TrackLineage | Enables 3D and 4D object tracking; track motion & morphology changes in live images; detect divisions, create lineage tree |
| Filament Tracer | Allows for the detection, tracing and analysis of filament like structures in 3D; trace neurons, vessels, mitochondria, detect spines |
In addition to the Leica LAS X and Imaris products, the off-line workstation also has ImageJ/FIJI and both the Adobe Suite (e.g., Photoshop CC 2018) and Microsoft Office Suite (Word, Excel, PowerPoint, etc.) of products.
Currently, there is no formal training scheduled for the Leica LAS-X and Imaris software, but there are many helpful on-line webinar videos (for Imaris), and users can request personalized help/training from Leica and Bitplane. A reference manual and quick start tutorials for Imaris 9.6 can be found on the workstation. Contact Dr. Dailey if you are interested in links to Imaris webinars, or more personalized help.
Reserving time on the off-line workstation
All users should reserve time on the system in the same way they reserve time for the confocal microscopes.