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Image Analysis Software

Image Analysis Software

Soleus Muscle
Mouse Soleus muscle stained for g-actin (Green), a-actinin (Red), phalloidin (yellow) and Hoechst (Blue).  Confocal image stacks taken on the Zeiss LSM 710 and reconstructed in Volocity (R. Nowak, V. 

Volocity Software

Volocity® 3D Image Analysis Software from Perkin Elmer allows visualization and rendering of volumes of large confocal Z stacks of images of cells or tissues.   Volocity can compare and relate areas of interest within and between samples, perform morphological analysis, measure and quantify fluorescence localization and calculate a colocalization index with Pearson’s coefficients, measure distances within stacks, track object movements automatically or manually, create charts and graphs, and export data for further analysis.

 

Distributed Deconvolution (DDecon) Software

DDecon is an immunofluorescence-based computational image analysis technique that is used to analyze the positions and breadths of fluorescent signals along striated myofibrils (1).  DDecon operates as a custom-made plugin for ImageJ, whereby theoretical intensity distribution functions for various myofibrillar components are fitted to experimental 1D myofibril fluorescence intensity profile (line scans) via an iterative and multivariate line-fitting algorithm (1).  The primary application of DDecon is high-precision measurement of thin filament lengths, which can be achieved using either isolated myofibrils or tissue cryosections from a host of vertebrate species, including birds, rodents, and humans (1-4).  Ongoing work will expand DDecon’s repertoire of functions to include integration of fluorescence signal intensity along a line scan in order to enable ratiometric comparisons of fluorescence intensities at different positions along a myofibril.

Line Scan analysis

Screen shot of Line Scan analysis interface in Distributed Deconvolution software (D. Gokhin, Z. Ren, V. Fowler). 

References

  1. Littlefield, R., and Fowler, V. M. (2002) Measurement of thin filament lengths by distributed deconvolution analysis of fluorescence images. Biophys J 82, 2548-2564
  2. Castillo, A., Nowak, R., Littlefield, K. P., Fowler, V. M., and Littlefield, R. S. (2009) A nebulin ruler does not dictate thin filament lengths. Biophys J 96, 1856-1865
  3. Gokhin, D. S., Kim, N. E., Lewis, S. A., Hoenecke, H. R., D'Lima, D. D., and Fowler, V. M. (2012) Thin-filament length correlates with fiber type in human skeletal muscle. Am J Physiol Cell Physiol 302, C555-565
  4. Gokhin, D. S., Lewis, R. A., McKeown, C. R., Nowak, R. B., Kim, N. E., Littlefield, R. S., Lieber, R. L., and Fowler, V. M. (2010) Tropomodulin isoforms regulate thin filament pointed-end capping and skeletal muscle physiology. J Cell Biol 189, 95-109