2012-01-19 - New Release of Stitching

QR for this page

From Fiji

Jump to: navigation, search

You can now reconstruct arbitrarily sized, tiled acquisitions (which can be multi-channel, time-lapse stacks) with just very little RAM (even <1GB) if you activate the options to write the result directly to disk and/or open the input stacks only virtually!!

Here is a list of all new highlights:

  • supports composite images and hyperstacks now (arbitrary amount of channels and time-points)
  • can optionally write the stitched image slice-by-slice directly to disk (significantly reduces the RAM requirements)
  • can optionally open the input images as Virtual Stacks (significantly reduces the RAM requirements)
  • supports timelapse alignment with different stitching options
  • subpixel-resolution
  • supports many different types of grids (row-by-row, column-by-column, snake, ...)
  • can read the approximate tile positions from the image metadata
  • finally based on ImgLib

There are only two plugins left, they replace the Stitching2D/3D and the Stitch Grid, ... Sequence, ... Collection and so on. They are called:

  • Stitching -> Pairwise Stitching
  • Stitching -> Grid/Collection Stitching

You will find a complete documentation on the Fiji wiki: Image_Stitching

The Stitching is deployed as a component of Fiji (simply update Fiji) or you can download it for ImageJ as a stand-alone package which includes all necessary libraries (11MB): Download...

I thank all the authors of the libraries and other people who helped me with the Stitching: Acknowledgements

Last but not least, it would be really nice if you could cite the publication that is associated with the plugin:

  • S. Preibisch, S. Saalfeld, P. Tomancak (2009) "Globally optimal stitching of tiled 3D microscopic image acquisitions", Bioinformatics, 25(11):1463-1465. Webpage PDF