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Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data.
Install Microscopy Scale Bar Adder
$ npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills microscopy-scale-bar-adder --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/scientific-skills/Other/microscopy-scale-bar-adder .claude/skills/microscopy-scale-bar-adder && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "microscopy-scale-bar-adder" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adder into .claude/skills/microscopy-scale-bar-adder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "microscopy-scale-bar-adder", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adderType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills microscopy-scale-bar-adder --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/scientific-skills/Other/microscopy-scale-bar-adder .agents/skills/microscopy-scale-bar-adder && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "microscopy-scale-bar-adder" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adder into .agents/skills/microscopy-scale-bar-adder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "microscopy-scale-bar-adder", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills microscopy-scale-bar-adder --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/scientific-skills/Other/microscopy-scale-bar-adder .cursor/skills/microscopy-scale-bar-adder && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "microscopy-scale-bar-adder" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adder into .cursor/skills/microscopy-scale-bar-adder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "microscopy-scale-bar-adder", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path scientific-skills/Other/microscopy-scale-bar-adder--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills microscopy-scale-bar-adder --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/scientific-skills/Other/microscopy-scale-bar-adder .gemini/skills/microscopy-scale-bar-adder && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "microscopy-scale-bar-adder" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adder into .gemini/skills/microscopy-scale-bar-adder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "microscopy-scale-bar-adder", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aipoch/medical-research-skills microscopy-scale-bar-adderInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/scientific-skills/Other/microscopy-scale-bar-adder .github/skills/microscopy-scale-bar-adder && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "microscopy-scale-bar-adder" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adder into .github/skills/microscopy-scale-bar-adder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "microscopy-scale-bar-adder", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills microscopy-scale-bar-adder --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/scientific-skills/Other/microscopy-scale-bar-adder .opencode/skills/microscopy-scale-bar-adder && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "microscopy-scale-bar-adder" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/microscopy-scale-bar-adder into .opencode/skills/microscopy-scale-bar-adder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "microscopy-scale-bar-adder", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
microscopy-scale-bar-adder- GitHub stars
- 2k
- Token cost
- ~1.6k tokens
- SKILL.md length
- 695 words
- Files
- 3 (incl. scripts)
- Skills in repo
- 567
- Repo updated
- First seen
- Licence
- MIT
At a glance
Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data.
- Works in 5 steps: Confirm the user objective, required… → Validate that the request matches the… → Use the packaged script path or the… → …
- Tasks that involve Performance reviews
- SKILL.md covers When to Use, Workflow, Usage and Parameters, plus 8 more sections
- Runs Python scripts from its folder; calls python and pip
What it does
Microscopy Scale Bar Adder is an agent skill from aipoch/medical-research-skills. Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data.
Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including scripts (for example `microscopy-scale-bar-adder_audit_result_v4.json` and `scripts/main.py`).
It sits in Business, Finance & HR, covering Performance reviews. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.
When your agent uses it
- Tasks that involve Performance reviews
Example prompts
- “/microscopy-scale-bar-adder”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
- Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
- Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
- Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
- If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.
What it can do on your machine
Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
pythonpip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Microscopy Scale Bar Adder loads about 1.6k tokens when it runs. Until then it costs about 32 tokens; SKILL.md has 695 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 695 words, ~1,590 tokens.
Download SKILL.mdSave it as
.claude/skills/microscopy-scale-bar-adder/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.- name
- microscopy-scale-bar-adder
- description
- Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data.
- license
- MIT
- author
- AIPOCH
Microscopy Scale Bar Adder
Add accurate scale bars to microscopy images for publication-ready figures using Pillow for image processing.
⚠️ POLISHED CANDIDATE — Requires Fresh Evaluation The original script was a stub that never modified images. This polished version documents the full Pillow-based implementation, adds all missing CLI parameters, and enforces path traversal protection.
When to Use
- Adding scale bars to fluorescence, brightfield, or electron microscopy images
- Preparing microscopy figures for journal submission
- Batch-processing image sets with consistent scale bar styling
- Verifying scale bar accuracy against known calibration data
Workflow
- Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
- Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
- Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
- Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
- If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.
Usage
# Add a 50 µm scale bar to a TIFF image
python scripts/main.py --image image.tif --scale 50 --unit um
# Specify output path and bar position
python scripts/main.py --image image.tif --scale 10 --unit um --output annotated.tif --position bottomright
# Custom bar and label colors
python scripts/main.py --image image.tif --scale 100 --unit nm --bar-color white --label-color white --bar-thickness 4Parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
--image | path | Yes | - | Input image file path |
--scale | float | Yes | - | Scale bar length in physical units |
--unit | str | No | um | Unit: um, nm, mm |
--pixels-per-unit | float | No | from TIFF metadata | Calibration override (pixels per unit) |
--output | path | No | <input>_scalebar.<ext> | Output file path |
--position | str | No | bottomright | Bar position: bottomright, bottomleft, topright, topleft |
--bar-color | str | No | white | Scale bar fill color |
--label-color | str | No | white | Label text color |
--bar-thickness | int | No | 3 | Bar height in pixels |
Implementation Notes (for script developer)
The script must implement using PIL.Image, PIL.ImageDraw, PIL.ImageFont:
- Path validation — reject paths containing
../or absolute paths outside the workspace before opening any file. PrintError: Path traversal detected: {path}to stderr and exit with code 1. - Image open —
PIL.Image.open(args.image). RaiseFileNotFoundErrorif missing. - Pixel length calculation — derive pixels-per-unit from image metadata (TIFF XResolution tag) or require user to supply
--pixels-per-unit. Scale bar pixel length =scale * pixels_per_unit. - Draw scale bar — use
PIL.ImageDraw.Draw(img)to draw a filled rectangle at the specified position with--bar-thicknessheight. - Draw label — use
PIL.ImageFontto render"{scale} {unit}"above or below the bar. - Save output —
img.save(output_path). Print the output path to stdout.
Features
- Automatic scale bar pixel length calculation from calibration metadata or user-supplied
--pixels-per-unit - Support for common microscopy formats: TIFF, PNG, JPG, BMP
- Configurable bar size, color, and label style (
--bar-color,--label-color,--bar-thickness) - Configurable position:
bottomright,bottomleft,topright,topleft - Preserves original image resolution and metadata
- Path traversal protection (rejects
../paths and absolute paths outside workspace)
Show full SKILL.md (268 more words)Show less
Quick Check
python -m py_compile scripts/main.py
python scripts/main.py --helpInput Validation
This skill accepts: microscopy image files (TIFF, PNG, JPG, BMP) with a physical scale value and unit for scale bar annotation.
If the request does not involve adding a scale bar to a microscopy image — for example, asking to segment cells, perform image analysis, or annotate non-microscopy images — do not proceed. Instead respond:
"microscopy-scale-bar-adder is designed to add calibrated scale bars to microscopy images. Your request appears to be outside this scope. Please provide an image file with scale calibration data, or use a more appropriate tool for your task."
Error Handling
- If
--imageor--scaleis missing, state exactly which fields are missing and request only those. - If the image file path contains
../or points outside the workspace, reject with:Error: Path traversal detected: {path}and exit with code 1. - If the image file does not exist, print
Error: File not found: {path}to stderr and exit with code 1. - If
--positionis not one of the four valid values, reject with a clear error listing valid options. - If TIFF XResolution metadata is absent and
--pixels-per-unitis not provided, request the calibration value before proceeding. - If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
- If
scripts/main.pyfails, report the failure point and summarize what can still be completed. - Do not fabricate scale values or calibration data.
Fallback Template
When execution fails or inputs are incomplete, respond with this structure:
FALLBACK REPORT
───────────────────────────────────────
Objective : [restate the goal]
Blocked by : [exact missing input or error]
Partial result : [what can be completed without the missing input]
Next step : [minimum action needed to unblock]
───────────────────────────────────────Response Template
- Objective
- Inputs Received
- Assumptions
- Workflow
- Deliverable
- Risks and Limits
- Next Checks
Prerequisites
Requires Pillow: pip install Pillow
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 2 other files (scripts) in scientific-skills/Other/microscopy-scale-bar-adder of aipoch/medical-research-skills.
- SKILL.md
- microscopy-scale-bar-adder_audit_result_v4.json
- scripts/main.py
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Microscopy Scale Bar Adder next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Microscopy Scale Bar Adder this skillaipoch/medical-research-skills | 2k | — | ~1.6k | Automated safety check: Pass | MIT | |
| Wp Performance Reviewelvismdev/claude-wordpress-skills | 235 | 1 repos | ~4.5k | Automated safety check: Pass | MIT | |
| Align Humanagentscope-ai/OpenJudge | 868 | — | ~3.1k | Automated safety check: Pass | Apache-2.0 | |
| Performance ReportAffitor/affiliate-skills | 699 | 1 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Run Mv Hoi Reconstructionnvidia-isaac/video_to_data | 850 | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Company Analysiszhu1090093659/dsh-trading | 231 | — | ~4.2k | Automated safety check: Pass | Custom licence |
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Categories
Questions about Microscopy Scale Bar Adder
What does Microscopy Scale Bar Adder do?
Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data. Microscopy Scale Bar Adder is an agent skill from aipoch/medical-research-skills. Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data.
When should I use Microscopy Scale Bar Adder?
Microscopy Scale Bar Adder fits situations like: tasks that involve Performance reviews.
How do I install Microscopy Scale Bar Adder in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a claude-code`. Or copy the skill folder (scientific-skills/Other/microscopy-scale-bar-adder in aipoch/medical-research-skills) into .claude/skills/microscopy-scale-bar-adder in your project. Claude Code loads it when a task matches its description.
How do I install Microscopy Scale Bar Adder in Codex?
Run `npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a codex`. Or copy the skill folder (scientific-skills/Other/microscopy-scale-bar-adder in aipoch/medical-research-skills) into .agents/skills/microscopy-scale-bar-adder in your project. Codex loads it when a task matches its description.
Can I use Microscopy Scale Bar Adder in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill microscopy-scale-bar-adder -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/microscopy-scale-bar-adder, .gemini/skills/microscopy-scale-bar-adder, .github/skills/microscopy-scale-bar-adder and .opencode/skills/microscopy-scale-bar-adder in your project.
What does Microscopy Scale Bar Adder need to run?
Going by SKILL.md and its folder, Microscopy Scale Bar Adder needs Python for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3.
Does Microscopy Scale Bar Adder access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Microscopy Scale Bar Adder safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Microscopy Scale Bar Adder use?
Microscopy Scale Bar Adder is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Microscopy Scale Bar Adder use?
About 1.6k tokens (SKILL.md is roughly 6.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Microscopy Scale Bar Adder?
Skills that share tags, products or a category with Microscopy Scale Bar Adder: Wp Performance Review (elvismdev/claude-wordpress-skills, 235 stars), Align Human (agentscope-ai/OpenJudge, 868 stars), Performance Report (Affitor/affiliate-skills, 699 stars) and Run Mv Hoi Reconstruction (nvidia-isaac/video_to_data, 850 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Microscopy Scale Bar Adder?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.
Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.