Imaris Stitcher

30.7.2020 In preparation.

Imaris Stitcher is an excellent tool to for stitching large 3D data sets. It requires that every tile is its own ims file. So usually you first have to convert your microscope images into ims-format by ImarisFileConverter.

Unfortunately ome.tiff files from Aurox Clarity have to be converted to normal tiff-format first.

Open ompanion.ome file of your tile by Fiji Hyperstack and choose Group files with similar names and Concatenate series when compatible and select6 all tiffs. This should result One image window with slicers for z- channel and positions as time. The example does not have stacks.

Save tiffs by Save as / Image sequence. This will create separate tiff for every slice, channel and time (position). Save tiffs in their own folder.

Then convert tiffs to ims files using ImarisFileConverter

Choose first tiff of the tile and add it as an input. Select the file and click Settings. You have to choose the correct format your tiff file names has. For the positions use F(Split):

Click ok for Settings. Start All starts the converting and you should get one ims-file per tile position in the folder you specified in Output. Default is same folder were the input files were.

Start Imaris Stitcher