Is the Trackpy Particle Tracking skill free?

Yes. The skill itself is free from jaechang-hits/SciAgent-Skills. SkillProof publishes the install command and an independent test verdict at no cost.

What is the Trackpy Particle Tracking SkillProof Score?

9.2/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 8/10, docs & honesty 5/5.

How do I install Trackpy Particle Tracking?

Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.

Can I use Trackpy Particle Tracking with Cursor, Copilot, Gemini CLI, Codex or other AI tools?

The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.

Trackpy Particle Tracking

Single-particle tracking in microscopy video: locate, link, filter, MSD diffusion with trackpy

by jaechang-hits · jaechang-hits/SciAgent-Skills

Tested · Works

Install — copy the command Download source ↗

Test report

Verdict: Tested · Works
Score: 9.2/10
Tested: Jul 31, 2026
Environment: Claude Code 2.x (agent harness)
Upstream re-checked: Aug 10, 2026 · 3a575ed

Fetched SKILL.md (only file in the dir; no bundled scripts, no security smells; frontmatter has name+description, license BSD-3). Installed trackpy 0.7 + pims in a venv, generated a synthetic 60-frame TIF of 25 Gaussian particles doing a random walk with known D_true=0.8 px^2/frame. Ran a BASELINE script (guessed diameter, default minmass, no stub filter, no drift correction, crude lag-1 MSD) and a SKILL script (Workflow 1 verbatim: locate tune, batch processes=1, link+memory, filter_stubs, compute_drift/subtract_drift, emsd linear-regime fit). Baseline over-detected noise (~55 features/frame vs 25 real), fragmented into 1752 tracks, and returned D=1.259 (57% high); the skill filtered to 20 clean tracks and returned D=0.691 (R^2=0.998), much closer to truth. All documented API calls (locate, batch, link, filter_stubs, compute_drift, subtract_drift, emsd) executed correctly.

Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works

Installs cleanly 5/5
Triggers reliably 5/5
Output vs. baseline 8/10
Docs & honesty 5/5

What Trackpy Particle Tracking does

A reference skill for the Python trackpy library that walks Claude through single-particle tracking (SPT) in video microscopy: locating bright spots per frame, linking them into trajectories, filtering short tracks, correcting stage drift, and computing MSD to extract diffusion coefficients in 2D and 3D. Triggers when a user has a fluorescence or brightfield microscopy video (TIF stack, AVI, image series) and wants per-particle trajectories, mean squared displacement curves, or diffusion coefficients. Does not trigger for image segmentation, cell counting, or generic object detection.

How to install Trackpy Particle Tracking

git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git /tmp/trackpy-particle-tracking-src
mkdir -p ~/.claude/skills
cp -R /tmp/trackpy-particle-tracking-src/skills/cell-biology/trackpy-particle-tracking ~/.claude/skills/trackpy-particle-tracking
# Runtime deps (skill is doc-only, no bundled scripts):
#   pip install trackpy pims pandas numpy matplotlib scipy
# For ND2/CZI/LIF microscopy formats: pip install pims-nd2  OR  pip install aicsimageio
# Verified with trackpy 0.7 in a clean venv.

Skills live in ~/.claude/skills/ (global) or .claude/skills/ (per-project). Restart Claude Code after installing.

Commands — how to trigger Trackpy Particle Tracking

/trackpy-particle-tracking Single-particle tracking in microscopy video: locate, link, filter, MSD diffusion with trackpy

It also activates on plain-language prompts like these:

Track fluorescent particles in this microscopy video
Compute MSD for these vesicle trajectories
Link detected spots into particle tracks across frames

Frequently asked questions

Is the Trackpy Particle Tracking skill free?: Yes. The skill itself is free from jaechang-hits/SciAgent-Skills. SkillProof publishes the install command and an independent test verdict at no cost.
Does Trackpy Particle Tracking work with Claude Code?: We tested it with Claude Code 2.x (agent harness) on Jul 31, 2026. Verdict: Tested · Works. Fetched SKILL.md (only file in the dir; no bundled scripts, no security smells; frontmatter has name+description, license BSD-3). Installed trackpy 0.7 + pims in a venv, generated a synthetic 60-frame TIF of 25 Gaussian particles doing a random walk with known D_true=0.8 px^2/frame. Ran a BASELINE script (guessed diameter, default minmass, no stub filter, no drift correction, crude lag-1 MSD) and a SKILL script (Workflow 1 verbatim: locate tune, batch processes=1, link+memory, filter_stubs, compute_drift/subtract_drift, emsd linear-regime fit). Baseline over-detected noise (~55 features/frame vs 25 real), fragmented into 1752 tracks, and returned D=1.259 (57% high); the skill filtered to 20 clean tracks and returned D=0.691 (R^2=0.998), much closer to truth. All documented API calls (locate, batch, link, filter_stubs, compute_drift, subtract_drift, emsd) executed correctly.
What is the Trackpy Particle Tracking SkillProof Score?: 9.2/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 8/10, docs & honesty 5/5.
How do I install Trackpy Particle Tracking?: Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
Can I use Trackpy Particle Tracking with Cursor, Copilot, Gemini CLI, Codex or other AI tools?: The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.