Drag_Force_Analysis/README_DragAuto.md

Drag Auto — Drag Force Analysis

Loads particle centroid tracking data, lets you interactively define movement regions, and computes drag force vs. displacement with a linear fit per particle and direction.

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Workflow Overview

1. Load CSVs — Reads all *.csv files from a folder (output from Drag Force Particle Tracking Automatic.ipynb). Automatically detects the number of particles from the column count (3 columns per particle: cx, cy, r).

2. Set regions (slider cell) — For each speed, an interactive plot shows the x-position traces for all particles over time. Use the three sliders to define:

   • Stationary — frames where the stage is not moving (baseline)
   • Movement 1 — first direction of stage movement
   • Movement 2 — second direction of stage movement (return)

   Click Confirm All & Continue when all speeds are set.

3. Analyze — Computes the mean displacement of each particle relative to its stationary baseline, and the expected Stokes drag force at each speed. Fits a linear spring constant k (pN/µm) per particle per direction through the origin.

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Key Parameters (Analysis Cell)

Parameter	Description
folder	Path to folder containing {speed} mms.csv files
PIXELS_PER_MICRON	Pixel-to-micron conversion factor
ETA	Fluid viscosity (Pa·s); default: 0.001 (water)
R	Particle radius (m); default: 1e-6 (1 µm)
TRIM	Frames trimmed from each edge of a region to remove transients

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Output Plot

• Color = particle (each particle gets a unique color)
• Filled circles = Direction 1 (Movement 1), open circles = Direction 2 (Movement 2)
• Solid fit line = Direction 1, dotted fit line = Direction 2
• Separate origin-constrained fit per particle per direction with 95% confidence interval shading
• Printed spring constant k ± σ (pN/µm) for each particle and direction

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Input File Format

CSV files must match the output of Drag Force Particle Tracking Automatic.ipynb:

• No header row
• Filename: {speed} mms.csv (e.g. 0.25 mms.csv)
• Columns: cx0, cy0, r0, cx1, cy1, r1, cx2, cy2, r2 (3 per particle, up to 3 particles)

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Dependencies

numpy, pandas, scipy, matplotlib, ipywidgets, ipympl

Install missing packages with pip install <package>.

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Tracking Data Source

Generate input CSVs using Drag Force Particle Tracking Automatic.ipynb.