Scanning Time


I was wondering if anyone has experience or an idea how long it takes to scan an entire brain? In addition, what software was used? There is an freeware available that seems to be promising:

Thank you for everyone's ideas.


  • FabioFabio Posts: 62
    edited December 2013
    I think these all depends on your settings. Which resolution, how big is the scan area, which kind of objective, the frame average, what kind of stage do you have.

    For me with my actual settings a 1.55 mm x 1.55 mm x 1.55 mm area takes 3h.
    In my opinion for a whole brain you should prepare yourself for running it several days.

    I am using imaris right now and doing deconvolution with huygens.
    Ill check out that program thanks
  • Hi Fabio,
    Thanks for sharing your experience.

    What magnification do you use? I was considering to use 100-200x on a Leica confocal TCS SP5.
  • FabioFabio Posts: 62
    im using a 10x water obj WD 3.6 mm (like in the publication), also on a TCS SP5
  • Great! Thanks a lot.
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