OCT_brush

This repository contains processing pipelines for Optical Coherence Tomography (OCT) data acquired in brush-related experiments.
It includes scripts to process structural scans, vibration videos, morph data, phase-change maps, and skin-surface tracking.

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Folder Structure

├─ 1_process/
│ └─ OCT/
│ ├─ 1_0_0_process_oct_structural_images.py
│ ├─ 1_1_1_process_oct_video_vibrations.py
│ ├─ 1_1_1_process_oct_video_vibrations_4saito.py
│ ├─ 1_1_3_process_oct_video_vibrations_show.py
│ ├─ 1_2_1_process_oct_video_vibration_as_image.py
│ ├─ 1_3_0_process_oct_phase-change.py
│ ├─ 1_3_1_process_oct_morph-n-phase-change_show.py
│ └─ 1_4_0_process_oct_skin-surface_tracking.py
└─ library_python/ (utility modules used across scripts)

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Scripts Overview (OCT)

• 1_0_0_process_oct_structural_images.py
  Processes structural OCT acquisitions into normalized 16-bit grayscale morph images.

• 1_1_1_process_oct_video_vibrations.py
  Computes morphological data for non-structural vibration recordings and saves results.

• 1_1_1_process_oct_video_vibrations_4saito.py
  Estimates skin displacement from vibration videos by depth filtering and boundary detection; exports CSV and optional figures.

• 1_1_3_process_oct_video_vibrations_show.py
  Loads processed vibration data (morph.pkl), applies optional resizing/smoothing/detrend/flip/normalization, and visualizes A-line surfaces or subplots.

• 1_2_1_process_oct_video_vibration_as_image.py
  Converts vibration volumes to per-A-line images with optional downsampling; exports a multi-page TIFF stack.

• 1_3_0_process_oct_phase-change.py
  Runs phase-change computation on vibration recordings and saves the results as phase_change_data.npy.

• 1_3_1_process_oct_morph-n-phase-change_show.py
  Visualizes amplitude (dB), phase, and phase-change images per A-line; exports PNGs (packable into _all_morph_and_phase/).

• 1_4_0_process_oct_skin-surface_tracking.py
  Tracks the skin surface in vibration videos by denoising and binarizing depth-time slices; saves positions to skin_displacement_estimation.csv.

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Requirements

• Python 3.9+
• Core libraries: numpy, pandas, matplotlib, opencv-python, scipy, scikit-image, tifffile
• Custom modules: library_python (included in this repo)

Install dependencies:

pip install -r requirements.txt