DOI: 10.1093/bioinformatics/btae041 ISSN: 1367-4803

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties

Diogo A C Narciso, Ana Pereira, Nuno O Dias, Manuel Monteiro, Luis F Melo, Fernando G Martins
  • Computational Mathematics
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability



BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices.


Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis.

Availability and implementation

BISCAP is available from All images used in the tutorials and the validation examples are available from∼fgm/biscap3d.

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