This Windows 10 workstation (HP Z820 with 8 Xeon cores and 128GB of RAM) is set up to run HCImage (Hamamatsu). HCImage can be configured with macros that allow the software to do semi-automated image analysis (using thresholding and segmentation) of image data from the DMI6000 microscope, or images from other sources. For calibrating images from other optical microscopes, Mr. Cromey has a stage micrometer that users can borrow. Numerical data from image analysis measurements can be exported as CSV files for further analysis (CSV files can be imported into MS Excel).
To use the workstation, contact Mr. Cromey first to discuss your image analysis needs. The workstation is free to use, however, if a macro needs to be built for your lab’s analysis, there may be several hours of billable labor involved to write it.
Other possible uses of this workstation include video editing and working with large files that might be too big to work with on standard lab computers/laptops. With the assistance of our IT team, the data directory on the Zeiss Axio Observer 7 with Apotome III and the Leica DMI6000 have been mapped so that they can be read on this workstation (read only access), allowing users to pull their data directly to this computer worktation if needed.
Software currently installed on this workstation (Jan 2023):
- HCImage 4.7 (initially purchased by the SWEHSC, P30 ES006694)
- ImageJ (FIJI) (open source image analysis software)
- Cell Profiler (open source image analysis software)
- Qu-Path (open source whole slide image analysis software)
- Free viewer software (Zeiss ZEN Blue, Nikon Elements viewer, Leica LAS X, Olympus viewer software, Aperio Scanscope)
- Adobe Creative Cloud (including Photoshop, Premier Pro) - (NOTE: you may need to have a license for these associated with your UA netID, if needed you can request access to Doug Cromey's license)
- Image data management resources:
- OMERO.insight (open source software for connecting to the campus OMERO server)
- CISCO AnyConnect (required for the UA VPN)
- Glencoe NGFF-converter (capable of batch transforming specific proprietary file formats into OME-TIF files, which may be required before they can be uploaded to the campus OMERO server)
