Segmentation Biomarker CTC

Algorithm for the segmentation of prostate-specific membrane antigen labeling in circulating tumor cells (CTCs) of metastatic patients I designed and partially implemented.

Quick start

This repository covers segmentation of PSMA-labeled CTCs at two resolutions, plus a set of general-purpose supporting tools. See DEPENDENCIES.md for the Matlab Compiler Runtime requirement of the compiled executables.

Repository contents

• coverslip/ -- the main analysis code, covering both coverslip and Gedi-chip samples:
  • high_resolution/ -- WaveletSeedingWatershedActiveContour/ (the wavelet-seeding + active-contour + watershed segmentation algorithm).
  • low_resolution/ -- find_ctc.exe / optimal_ctc.exe (compiled low-resolution whole-slide analysis), codeCTC.zip, genOptimalCTC2.m, the .ini configuration files (covering both coverslip and Gedi-chip datasets), and run_optimal_detection_9283.bat.
  • Segmentation3D/ -- 3D segmentation code.
  • spotDetection/ -- bright-spot detection via stationary wavelet transform.
  • The Matlab scripts at this folder's top level (CTCQ_*.m, Coverslips_new_code.m) are the high-resolution cropped-image analysis.
• additional_tools/ -- general-purpose tools used across the project, not specific to coverslip/chip samples:
  • SVM/ -- Support Vector Machine classification code.
  • HoughTransform/ -- Hough Transform line/circle detection code (see that folder's own README for its specific license terms).
• media/ -- supplementary video, image, and PDF files.
• License: see LICENSE -- research/educational use, with separate terms noted for bundled third-party components.

About

The patient blood samples analyzed were from clinical studies with IRB protocols 0804009740 and 0707009283 at Cornell Medicine and the NCT01718353 phase II clinical trial sponsored by Sanofi for early switch from docetaxel to cabazitaxel during the treatment of metastatic castrate-resistant prostate cancer; see the examples of image processing of whole slides in folder coverslip.

Watch my CTC presentation, the second part of this seminar, at the University of Central Florida in 2013: https://youtu.be/kTYyltX9RFg?t=1564

For detailed information, see: https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2025.1677302