Robust, globally consistent and fully automatic multi-image registration and montage synthesis for 3-D multi-channel images

C. L. Tsai, J. P. Lister, C. S. Bjornsson, K. Smith, W. Shain, C. A. Barnes, B. Roysam

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


The need to map regions of brain tissue that are much wider than the field of view of the microscope arises frequently. One common approach is to collect a series of overlapping partial views, and align them to synthesize a montage covering the entire region of interest. We present a method that advances this approach in multiple ways. Our method (1) produces a globally consistent joint registration of an unorganized collection of three-dimensional (3-D) multi-channel images with or without stage micrometer data; (2) produces accurate registrations withstanding changes in scale, rotation, translation and shear by using a 3-D affine transformation model; (3) achieves complete automation, and does not require any parameter settings; (4) handles low and variable overlaps (5-15%) between adjacent images, minimizing the number of images required to cover a tissue region; (5) has the self-diagnostic ability to recognize registration failures instead of delivering incorrect results; (6) can handle a broad range of biological images by exploiting generic alignment cues from multiple fluorescence channels without requiring segmentation and (7) is computationally efficient enough to run on desktop computers regardless of the number of images. The algorithm was tested with several tissue samples of at least 50 image tiles, involving over 5000 image pairs. It correctly registered all image pairs with an overlap greater than 7%, correctly recognized all failures, and successfully joint-registered all images for all tissue samples studied. This algorithm is disseminated freely to the community as included with the Fluorescence Association Rules for Multi-Dimensional Insight toolkit for microscopy ().

Original languageEnglish (US)
Pages (from-to)154-171
Number of pages18
JournalJournal of Microscopy
Issue number2
StatePublished - Aug 2011


  • 3-D microscopy
  • Image registration
  • Montage synthesis

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Histology


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