BiopTort

BiopTort is a tool designed for quantifying tortuosity in core needle biopsies. Tortuosity is a measure of the twisting and turning of the biopsy path, and is a common yet largely unreported artifact in pathology.

Features

BiopTort produces two types of output:

1. A .pptx file where each slide displays the qualitative BiopTort output:

2. A .csv file containing quantitative metrics extracted for each slide:

Installation

Using Docker

docker run -v <YOUR_DATA_PATH>:/data -it histotools/bioptort:main /bin/bash

Usage

BiopTort exposes the following CLI options:

bioptort --help

usage: bioptort [-h] --im_path IM_PATH --ppt_save PPT_SAVE [--csv_save CSV_SAVE] [--mask_path MASK_PATH] [--sort] [--gauss_sigma GAUSS_SIGMA] [--override_base_magnification OVERRIDE_BASE_MAGNIFICATION] [--multiple_sections]

optional arguments:
  -h, --help            show this help message and exit
  --im_path IM_PATH     The directory containing (openslide-compatible) CNB WSIs.
  --ppt_save PPT_SAVE   The path to save the powerpoint presentation, including the filename.
  --csv_save CSV_SAVE   Optional path to save a csv file containing quantitative results, including the filename.
  --mask_path MASK_PATH
                        Optional path to existing png tissue masks for the CNB WSIs with matching filenames.
  --sort, -s            Sort the slides in order of highest to lowest tortuosity.
  --gauss_sigma GAUSS_SIGMA
                        The sigma value for the gaussian filter.
  --override_base_magnification OVERRIDE_BASE_MAGNIFICATION
                        Manually specify the base magnification of the WSI if it cannot be read from the file properties.
  --multiple_sections, -m
                        Experimental: Enable handling of multiple sections per slide. May not work as intended.

An example command to run BiopTort is as follows:

bioptort --im_path /data/ --ppt_save /data/<YOUR_PPT_NAME>.pptx --csv_save /data/<YOUR_CSV_NAME>.csv

Citation

The related paper is published in the Archives of Pathology and Laboratory Medicine:

https://meridian.allenpress.com/aplm/article/doi/10.5858/arpa.2025-0028-OA/508037

Please use below to cite this paper if you find this repository useful or if you use the software shared here in your research.

Jacobs, J., Wiener, D., Pathak, T., Farré, X., Mirtti, T., & Janowczyk, A. , "Standardized Reporting of Core Needle Biopsy Tortuosity: BiopTort—A Computer-Aided Protocol for Categorizing Tortuosity", Arch Pathol Lab Med 2025; doi: https://doi.org/10.5858/arpa.2025-0028-OA

@article{10.5858/arpa.2025-0028-OA,
    author = {Jacobs, Jackson and Wiener, Dan and Pathak, Tilak and Farré, Xavier and Mirtti, Tuomas and Janowczyk, Andrew},
    title = {Standardized Reporting of Core Needle Biopsy Tortuosity: BiopTort—A Computer-Aided Protocol for Categorizing Tortuosity},
    journal = {Archives of Pathology & Laboratory Medicine},
    year = {2025},
    month = {10},
    issn = {0003-9985},
    doi = {10.5858/arpa.2025-0028-OA},
    url = {https://doi.org/10.5858/arpa.2025-0028-OA},
    eprint = {https://meridian.allenpress.com/aplm/article-pdf/doi/10.5858/arpa.2025-0028-OA/3543274/10.5858_arpa.2025-0028-oa.pdf},
}