Stitiching Ultra Microscope Files with Fiji

Owned by Ofra Golani
Last updated: Apr 20, 2017


There's a detailed instruction in the Ultra Microscope software manual: http://lvbt.de/software/ImspectorManual.pdf#subsection.13.1


in short:

  • In Fiji  select ’Plugins>Stitiching>Grid/Collection Stitching’
  • in the first window select ’Filename defined position’.


  • Setup stitching dialog (second window) according to the measurement:

- set up grid size
- set up same overlap that is used in Imspector
- select input directory
- set 'First File index' for x and y to 0

- Copy first file name of the series and change the position markers from:

     [00] x [00]
with
     {yy} x {xx}

When copying the file name make sure to copy the complete name incl. the '.tif' file extension!