What is Cabana?

CABANA (CollAgen Fibre ANAlyzer) is a specialized software tool developed for the analysis of collagen fiber architecture in biological images. It provides a comprehensive solution for researchers studying collagen structures in tissues through immunohistochemistry (IHC) and fluorescence microscopy.

Overview

Cabana combines several image processing techniques to detect, quantify, and analyze collagen fibers in microscopy images. The software processes images through multiple stages:

  1. Segmentation: Extracts regions of interest (ROIs) from the background based on color and other low-level features

  2. Ridge Detection: Identifies fiber structures using advanced ridge detection algorithms

  3. Orientation Analysis: Quantifies the orientation and alignment of fibers

  4. Skeleton Analysis: Evaluates the topological properties of fiber networks

  5. Gap Analysis: Measures spaces between and within fiber structures

Key Features

  • Compatible with both IHC (Picrosirius Red) and fluorescence microscopy images

  • Automated detection and quantification of collagen fibers

  • Analysis of fiber orientation, alignment, and distribution

  • Calculation of fiber thickness, length, and branching patterns

  • Gap analysis to quantify spaces within the fiber network

  • Comprehensive statistical outputs for quantitative analysis

  • Available in both desktop and cloud-based versions

Application Areas

Cabana is particularly useful for researchers in:

  • Cancer biology (studying tumor microenvironment)

  • Wound healing and tissue repair

  • Fibrosis research

  • Connective tissue disorders

  • Biomaterial development and evaluation

  • Regenerative medicine

Versions and Availability

Cabana is available in two versions:

  1. Desktop Version: For processing smaller datasets on local machines

  2. Google Cloud Version: For large-scale processing of datasets exceeding 10,000 images (currently available only to Garvan Institute staff and students)