Histolab Whole Slide Image Tiling
davila7/claude-code-templates
Processes digital pathology whole slide images with histolab: tissue detection, mask creation, tile extraction and dataset preparation for deep learning.
Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality…
Install Pyhealth
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill pyhealth -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills pyhealth --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/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/kdense/pyhealth .claude/skills/pyhealth && 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 "pyhealth" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealth into .claude/skills/pyhealth/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pyhealth", 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/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealthType 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 BioTender-max/awesome-bio-agent-skills --skill pyhealth -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills pyhealth --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/kdense/pyhealth .agents/skills/pyhealth && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pyhealth" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealth into .agents/skills/pyhealth/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pyhealth", 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 BioTender-max/awesome-bio-agent-skills --skill pyhealth -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills pyhealth --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/kdense/pyhealth .cursor/skills/pyhealth && 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 "pyhealth" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealth into .cursor/skills/pyhealth/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pyhealth", 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/BioTender-max/awesome-bio-agent-skills.git --path skills/kdense/pyhealth--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 BioTender-max/awesome-bio-agent-skills --skill pyhealth -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills pyhealth --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/kdense/pyhealth .gemini/skills/pyhealth && 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 "pyhealth" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealth into .gemini/skills/pyhealth/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pyhealth", 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 BioTender-max/awesome-bio-agent-skills pyhealthInstalls 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 BioTender-max/awesome-bio-agent-skills --skill pyhealth -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/kdense/pyhealth .github/skills/pyhealth && 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 "pyhealth" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealth into .github/skills/pyhealth/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pyhealth", 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 BioTender-max/awesome-bio-agent-skills --skill pyhealth -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills pyhealth --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/kdense/pyhealth .opencode/skills/pyhealth && 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 "pyhealth" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/kdense/pyhealth into .opencode/skills/pyhealth/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pyhealth", 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
pyhealth- GitHub stars
- 200
- Token cost
- ~1.8k tokens
- SKILL.md length
- 642 words
- Files
- 8 (incl. references, assets)
- Skills in repo
- 23
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality…
- Works in 6 steps: Models take a SampleDataset, not a… → Always split by patient (or visit), not… → Match the task to the dataset. Tasks are… → …
- The user mentions PyHealth
- SKILL.md covers When to use this skill, Installation (uv), The 5-stage pipeline and Critical things to get right, plus 2 more sections
- Runs Python scripts from its folder; calls uv; reaches storage.googleapis.com
What it does
Pyhealth is an agent skill from BioTender-max/awesome-bio-agent-skills. Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNorm lookup and…
Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including reference files and assets (for example `assets/starter_pipeline.py`, `references/datasets.md` and `references/examples.md`).
It sits in Research & Science, covering Clinical and healthcare research, Deep learning and MLOps. It works with Python. The repository describes itself as: A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
When your agent uses it
- The user mentions PyHealth
- Clinical prediction
- Drug recommendation
- Medical code mapping
Example prompts
- “PyHealth”
- “/pyhealth”
Requirements
- Python 3
Workflow steps
6 steps, taken from the first numbered list in SKILL.md.
- Models take a SampleDataset, not a BaseDataset. MIMIC3Dataset(...) returns a BaseDataset (a queryable patient registry). Only after…
- Always split by patient (or visit), not by sample. Random sample-level splits leak information across train/test because the same patient…
- Match the task to the dataset. Tasks are dataset-specific: MortalityPredictionMIMIC3 won't work on MIMIC-IV — use…
- Pick monitor to match the task type. For binary classification use "pr_auc" or "roc_auc". For multilabel (drug rec) use "pr_auc_samples"…
- MIMIC-IV uses ehr_root=, not root=. This is the one inconsistency in the dataset constructors.
- For reproducible work, point cache_dir= somewhere persistent. PyHealth caches the parsed dataset; without cache_dir, you re-parse every run.
What it can do on your machine
Read from SKILL.md and the folder at commit 8cbdd18. 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 script files (Python), which the agent can run.
Shell commands in SKILL.md call:
uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
storage.googleapis.com
Also links to:
pyhealth.dev
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
Pyhealth loads about 1.8k tokens when it runs, and up to ~9.4k if it reads all its reference files. Until then it costs about 213 tokens; SKILL.md has 642 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); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 642 words (~1,829 tokens).
“PyHealth (https://pyhealth.dev/) is a Python toolkit for clinical deep learning. It provides a unified, modular pipeline across electronic health records (EHR), physiological signals, and medical imaging.”
- name
- pyhealth
- metadata.skill-author
- K-Dense Inc.
Files
SKILL.md and 7 other files (references, assets) in skills/kdense/pyhealth of BioTender-max/awesome-bio-agent-skills.
- SKILL.md
- assets/starter_pipeline.py
- references/datasets.md
- references/examples.md
- references/installation.md
- references/medcode.md
- references/models.md
- references/tasks.md
Open the folder on GitHubat commit 8cbdd18
Compare with similar skills
Pyhealth 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 |
|---|---|---|---|---|---|---|
| Pyhealth this skillBioTender-max/awesome-bio-agent-skills | 200 | — | ~1.8k | Automated safety check: Pass | Custom licence | |
| Histolab Whole Slide Image Tilingdavila7/claude-code-templates | 33k | 11 repos | ~5.1k | Automated safety check: Pass | MIT | |
| PyHealth Clinical ML Toolkitdavila7/claude-code-templates | 33k | 11 repos | ~4.4k | Automated safety check: Pass | MIT | |
| Megatron-LM on SLURMNVIDIA/Megatron-LM | 18k | — | ~1.8k | Automated safety check: Pass | Apache-2.0 | |
| Rowanlamm-mit/scienceclaw | 246 | 4 repos | ~3.1k | Automated safety check: Warn | Proprietary | |
| pydicom DICOM Toolkitdavila7/claude-code-templates | 33k | 11 repos | ~3.3k | Automated safety check: Pass | MIT |
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Related
Works with
Categories
Questions about Pyhealth
What does Pyhealth do?
Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality…. Pyhealth is an agent skill from BioTender-max/awesome-bio-agent-skills.
When should I use Pyhealth?
Pyhealth fits situations like: the user mentions PyHealth; clinical prediction; drug recommendation; medical code mapping.
How do I install Pyhealth in Claude Code?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pyhealth -a claude-code`. Or copy the skill folder (skills/kdense/pyhealth in BioTender-max/awesome-bio-agent-skills) into .claude/skills/pyhealth in your project. Claude Code loads it when a task matches its description.
How do I install Pyhealth in Codex?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pyhealth -a codex`. Or copy the skill folder (skills/kdense/pyhealth in BioTender-max/awesome-bio-agent-skills) into .agents/skills/pyhealth in your project. Codex loads it when a task matches its description.
Can I use Pyhealth 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 BioTender-max/awesome-bio-agent-skills --skill pyhealth -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pyhealth, .gemini/skills/pyhealth, .github/skills/pyhealth and .opencode/skills/pyhealth in your project.
What does Pyhealth need to run?
Going by SKILL.md and its folder, Pyhealth needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Pyhealth access the network?
SKILL.md names 2 domains. In commands or code: storage.googleapis.com; the agent is likely to contact it when it follows the instructions. As links in the text: pyhealth.dev. This is read from the text; nothing was executed.
Is Pyhealth 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. Review the folder before installing.
What licence does Pyhealth use?
Pyhealth has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Pyhealth use?
About 1.8k tokens (SKILL.md is roughly 7.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 7.6k tokens, read only when the agent opens those files.
What are the alternatives to Pyhealth?
Skills that share tags, products or a category with Pyhealth: Histolab Whole Slide Image Tiling (davila7/claude-code-templates, 33k stars), PyHealth Clinical ML Toolkit (davila7/claude-code-templates, 33k stars), Megatron-LM on SLURM (NVIDIA/Megatron-LM, 18k stars) and Rowan (lamm-mit/scienceclaw, 246 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Pyhealth?
BioTender-max (a GitHub user) maintains it in BioTender-max/awesome-bio-agent-skills, which has 200 GitHub stars. The repository holds 23 skills in this directory. The repository was last updated on July 1, 2026.
Source: BioTender-max/awesome-bio-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.