BigStitcher Plugin Issue with Lightsheet Data


Hello Everyone,

I have used the BigStitcher plugin in FIJI to stitch together a lightsheet image of an embryo. While it did stitch the images, there are some issues: 1) The individual tiles don’t always overlap well/isn’t smooth 2) There are striations throughout the data. Here is a link to show everyone what I mean. Embryo image
I’m assuming I would need to adjust some parameters, but not sure what I would need to adjust.


  1. did you run stitch dataset and did you apply the global optimization?
  2. To me the striations you see appear to be rendering/interpolation artifact that arise as you are viewing a slice of the rotated volume Big Data viewer. If you export the volume using the Image Fusion dialog (right click in context menu) and look at this in a volume renderer you are probably not going to see these artefacts.