Lightsheet registration and fusion with Huygens

Last modified by hajaalin@helsinki_fi on 2024/01/24 07:08
  1. Deconvolution of individual illuminations
    • Deconvolution → Workflow processor
    • Add task
    • Create separate microscope settings for left and right.
    • Create deconvolution settings
    • Save as hdf5
  2. Fuse illuminations
    • Select I0_VX and I1_VX in main window.
    • Deconvolution → Interactive Fuser and Decon
    • Registration: "None" (illuminations have same view).
    • filename:I0_V0 + filename:I1_V0 → filename_V0
    • save result as hdf5 (optional)
  3. 3D registration and fusion of views
    • Select V0 ... VN in main window.
    • Deconvolution → Interactive Fuser and Decon
    • Main axis of rotation: Y
    • Rotation direction: counterclockwise
    • Color option: Global (to see all views simultaneously)
    • Shift in x and y directions as necessary.
    • Crop region as small as possible.
    • Registration options:
      • Options → Configure custom settings
        • Optimization ranges (try wider search if necessary, e.g. 10 deg, 55 px).
      • Click "Accept".
    • filename:V0 + filename_V1 → filename_fusion
    • save result as ICS
  4. Inspect in Imaris
    • First convert ICS → .ims with ImarisFileConverter.
    • Duplicate structures indicate that registration didn't work so well.