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FIbeR Extraction (FIRE) - A tool for extracting network architecture from 3D, confocal images of biopolymer networks

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FIbeR Extraction (FIRE)
Andrew M. Stein
March 5, 2009


FIRE is a Matlab tool for automatically extracting the network geometry for a
stack of confocal microscope images of a semiflexible polymer gel, such as
actin, fibrin or collagen. It works best when the polymer is fluorescently
labeled, though less good results can be achieved from reflectance images. The
is discussed in detail in:

  A.M. Stein, D.A. Vader, L.M. Jawerth, D.A. Weitz, and L.M. Sander.
  An algorithm for extracting the network geometry of 3d collagen gels.
  J. Microscopy, 232(3):463, 2008.

The manuscript is included with this documentation. The appendix lists the
parameters used by the algorithm. FIRE requires Matlab and the Matlab image
processing toolbox. To test the algorithm, open Matlab and change to the
FIRE/example directory in Matlab. Then, type "go example small" at the Matlab
prompt for a quick test (36 s on a 2 GHz MacBook Pro). For a larger data set,
run "go example" (19 min). When applying FIRE to new data sets, the user is
encouraged to start with small images and look at the plots generated by "go
example small" to understand what parameters should be altered to improve the


Thanks to D. Vader and D. Weitz for providing the images on which this has been
tested, and L. Sander, L. Jawerth, T. Jackson, P. Smereka, S. Esedoglu, and A.
Gilbert for many useful discussions. This work was supported by NIH
Bioengineering Research Partnership grant R01 CA085139-01A2 and the IMA.
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