Bio Image Processing Skills Index
- Repo stars 428
- Author updated Live
- Author repo PantheonOS
- Domain
- Engineering
- Compatible agents
-
- Claude Code
- Cursor
- Cline
- Codex
- Windsurf
- Gemini CLI
- +20
- Trust score
- 88 / 100 · community maintained
- Author / version / license
- @aristoteleo · no license declared
- Token usage
- Lean
- Setup complexity
- Plug-and-play
- External API key
- Not required
- Operating systems
- Unspecified (assume cross-platform)
- Runtime requirements
- No special requirements
- Permissions
-
- Read-only
- Write / modify
- Network behavior
- Local-only
- Install commands
- 26 variants
Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.
Heads up: 未限定 allowed-tools，默认拥有全部工具权限。
---
name: Bio Image Processing Skills Index
description: | Best practices and workflows for biological image analysis tasks including cell segmentation…
category: engineering
runtime: no special runtime
---
# Bio Image Processing Skills Index output preview
## PART A: Task fit
- Use case: | Best practices and workflows for biological image analysis tasks including cell segmentation, image restoration, and spatial data processing. Load the relevant skill files when performing specific analysis tasks. runs entirely locally. Works with Claude Code, Cursor, Cline and 23 more..
- Inputs: target material, constraints, expected output, and acceptance criteria.
- Evidence boundary: follow “Cell & Nucleus Segmentation / Using Skills” and do not present inference as author intent.
## PART B: Execution result
- **01** The card summarizes the use case; runtime output centers on “| Best practices and workflows for biological image analysis tasks including cell segmentation, image restoration, and spatial data processing. Load the relevant skill files when performing specific analysis tasks. runs entirely locally. Works with Claude Code, Cursor, Cline and 23 more.”.
- **02** When the source has headings, the agent prioritizes “Cell & Nucleus Segmentation / Using Skills” so the result follows the author’s structure.
- **03** Typical output includes task judgment, concrete steps, required commands or file edits, validation, and follow-up options.
- **04** Risk context follows the fingerprint: read files, write/modify files; mostly runs locally; usually needs no extra API key.
## Running Rules
- read files, write/modify files; mostly runs locally; usually needs no extra API key.
- Validate with a small sample before expanding scope.
- Return the result, validation criteria, and next iteration options.The source does not require a stable slash command. After installation, invoke the skill by name and describe the task.
Name target files or source material, expected output, forbidden changes, and whether network or shell access is allowed. Permission fingerprint: read files, write/modify files.
Start with a small task and check whether the result follows “Cell & Nucleus Segmentation / Using Skills”. Inspect diffs, logs, previews, or tests before expanding scope.
Confirm the final output includes a concrete result, evidence, and next action. If it stays generic, tighten inputs, boundaries, and acceptance criteria.
---
name: Bio Image Processing Skills Index
description: | Best practices and workflows for biological image analysis tasks including cell segmentation…
category: engineering
source: aristoteleo/PantheonOS
---
# Bio Image Processing Skills Index
## When to use
- | Best practices and workflows for biological image analysis tasks including cell segmentation, image restoration, and…
- Use it when the task has clear inputs, repeatable steps, and validation criteria.
## What to provide
- Target material, scope, expected result, and forbidden changes.
- Whether network, commands, file writes, or external services are allowed.
## Execution rules
- Organize steps around “Cell & Nucleus Segmentation / Using Skills” and keep inference separate from source facts.
- read files, write/modify files; mostly runs locally; usually needs no extra API key.
- Validate with a small sample before expanding the task.
## Output requirements
- Return the deliverable, key evidence, validation method, and next action.
- Mark missing information as unknown; do not invent commands, platforms, or dependencies.The author source anchors workflow facts; repository files anchor sources and commands; Fluxly only adds fit, limitations, and quality judgment.
skill "Bio Image Processing Skills Index" {
input -> user goal + target files + boundaries + acceptance criteria
context -> Cell & Nucleus Segmentation / Using Skills
rules -> SKILL.md triggers / order / output contract
runtime -> no special runtime | read files, write/modify files | mostly runs locally
guardrails -> usually needs no extra API key + small-sample validation + diff/log review
output -> copyable result + checklist + next iteration
}Agent Skills for Biological Image Processing
Best practices and workflows for biological image analysis tasks including cell segmentation, image restoration, and spatial data processing. Load the relevant skill files when performing specific analysis tasks.
Cell & Nucleus Segmentation
Tools and workflows for instance segmentation of cells and nuclei in microscopy images. Covers deep-learning methods (Cellpose, SAM-based, StarDist) with guidance on model selection, GPU/CPU inference, fine-tuning, and 3D segmentation.
Skill index: segmentation/SKILL.md
Skills:
- Cellpose: General-purpose cell/nucleus segmentation (Cellpose 3, Cellpose-SAM)
- SAM-Based Methods: CellSAM, micro-sam, SAMCell for automatic and interactive segmentation
When to use:
- Segmenting cells or nuclei in fluorescence, brightfield, or phase contrast images
- Need instance masks from 2D or 3D microscopy data
- Comparing or selecting between segmentation tools for your imaging modality
- Fine-tuning a segmentation model on custom training data
Using Skills
- Before analysis: Scan this index for relevant skills
- Load skill file: Read the full skill document for detailed guidance
- Follow best practices: Use the code snippets and workflows provided
- Adapt as needed: Skills are templates; adjust for your specific data
Decide Fit First
Design Intent
How To Use It
Boundaries And Review