The hardware, software, and people behind the iScope system
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  The Hardware:
  • Microscopes - our three Zeiss Universals (Tall, Dark, and Handsome) are equipped with motorized XYZ stages from Applied Scientific Instrumentation, as well as Sony IEEE1394 digital cameras with 1280x960 resolution.

  • Slide Handler (not yet online) : A robotic slide handler with a 600-slide capacity is currently in its final prototyping stages. We plan to build a slide handler for each of our three microscopes, resulting in access to a total of 1800 slides. Click here to see a photograph of Michael Connolly's first prototype; please note that the current slide handler has changed quite a bit from these homespun beginnings :-).
  • Computer: Dell Optiplex - PIII @ 933 Mhz, 512 MB RAM, 2x40GB HD. Red Hat Linux 7.3
  • Additional I/O: 8-port PCI RS-232 serial card from ByteRunner for hardware device control, OHCI-compatible FireWire card for camera interfaces. BayTech RPC2 for automatic illumination control.

  • Mass Storage - Quantum SnapServer NAS; 480GB with RAID5 protection, for archiving image stacks.

The Software:

  • Server Software
    • Designed in-house, the iScope server software allows control of an arbitary number of attached microscopes.
    • "Users and groups" authentication model with separate access rules for each microscope.
    • When a microscope is idle, the system keeps the microscopes busy acquiring image stacks for remote stereology.
    • Incorporates fiducial information from the Mouse Brain Library to ensure alignment between video and navigational aids.
  • Client Software
    • Simple graphical user interface for scheduling time on the system, controlling microscopes, and doing stereology on previously acquired image stacks.
    • Available for Linux and Windows 98/2000/NT/XP/ME.

The People:

  • Michael Connolly (left, handsome) wrote the iScope server software and Gumbo, the client software for controlling iScopes.
  • Tony Capra (right, dashing) wrote Aria 3-D, the client software for online stereology, and helped to develop the iScope client-server protocols.
  • Christopher Vincent (not pictured, mysterious) implemented the scheduling in Gumbo and squashed the great onslaught of bugs.
  • Senhua Yu (member of Dr. Williams lab) currently developing and maintaining iScope server software, Gumbo and Aria 3-D, and contributed to Gumbo 2.2~ and Aria 3-D 1.2~. June 25, 2004