Alejandro1400
commented
4 hours ago - SOAX
SOAX is based under the method Stretching Open Active Contours (SOACs). For an input image multiple SOACs are initiallized. These evolve by moving, stretching, merging and forming junctions with one another. The final network topology is configured by cutting and joining contours such that SOACs do not end or bend sarply at junctions.
The software provides a great way for extracting and quantifying biopolymer networks imaged by confocal microscopy in 3D. It is accompanied by an optimization method for parameter selection.
After an initial try of the software we can detect that it is able to accurately detect what it calls 'snakes' but its quantitative analysis is more focused on cell mechanical properties. It outputs: Curvature, Length, Point density, radial orientation, spherical orientation. Unfortunately since our focus on fluorescent labeling, we are more interested on analyzing things that can give us an insight of degree of labeling, SNR. The outputs CSV isn't easy to post-process due to its output (Every file has different organization and has no snake index so it is hard to understand each filaments' properties)
Still have to check outputing the image if it is possible to analyze it. Not sure how automating the process would work...
- Paper: SOAX: A software for quantification of 3D biopolymer networks
- Software Download: SOAX
Initially we are using a ridge detection method to analyze the actin filament networks in cell images, but it has come to my attention that there is a field in actin fialments which uses Stretching Open Active Contours (SOACs) algorithms to study the filamentous biopolymer networks in cells imaged by confocal microscopy.
This issue is going to serve as a thread about the literature review.