Visual parameter optimisation for biomedical image processing

BMC Bioinformatics
A J PretoriusR A Ruddle

Abstract

Biomedical image processing methods require users to optimise input parameters to ensure high-quality output. This presents two challenges. First, it is difficult to optimise multiple input parameters for multiple input images. Second, it is difficult to achieve an understanding of underlying algorithms, in particular, relationships between input and output. We present a visualisation method that transforms users' ability to understand algorithm behaviour by integrating input and output, and by supporting exploration of their relationships. We discuss its application to a colour deconvolution technique for stained histology images and show how it enabled a domain expert to identify suitable parameter values for the deconvolution of two types of images, and metrics to quantify deconvolution performance. It also enabled a breakthrough in understanding by invalidating an underlying assumption about the algorithm. The visualisation method presented here provides analysis capability for multiple inputs and outputs in biomedical image processing that is not supported by previous analysis software. The analysis supported by our method is not feasible with conventional trial-and-error approaches.

References

Nov 2, 2006·Genome Biology·Anne E CarpenterDavid M Sabatini
Nov 8, 2008·IEEE Transactions on Visualization and Computer Graphics·Kresimir MatkovićHelwig Hauser
Mar 18, 2010·Nature Methods·Thomas WalterJean-Karim Hériché
Oct 27, 2010·IEEE Transactions on Visualization and Computer Graphics·Stefan Bruckner, Torsten Möller
Oct 29, 2011·IEEE Transactions on Visualization and Computer Graphics·Thomas Torsney-WeirSteven Bergner
Oct 29, 2011·IEEE Transactions on Visualization and Computer Graphics·A Johannes PretoriusRoy A Ruddle
Jan 31, 2013·IEEE Transactions on Medical Imaging·Sebastian StegerStefan Wesarg
Jul 13, 2013·IEEE Transactions on Visualization and Computer Graphics·Steven BergnerAhmed Saad
Sep 21, 2013·IEEE Transactions on Visualization and Computer Graphics·Thomas Schultz, Gordon L Kindlmann
Sep 12, 2015·IEEE Transactions on Visualization and Computer Graphics·Michael BehamJohannes Kehrer
Sep 12, 2015·IEEE Transactions on Visualization and Computer Graphics·Michael SedlmairTorsten Moller
Dec 1, 2012·IEEE Transactions on Visualization and Computer Graphics·M SedlmairT Munzner

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Citations

Nov 26, 2015·IEEE Transactions on Visualization and Computer Graphics·Tatiana von LandesbergerMeike Becker
Sep 4, 2015·BMC Bioinformatics·Jan AertsDaniel Weiskopf

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Software Mentioned

Paramorama2
CellProfiler
PhotoMesa
PhotoFinder

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