Bio Image Processing Skills Index
- Repo stars 428
- Author repo PantheonOS
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
- Fluxly category
- Engineering
- Author-declared agents
- No explicit declaration found; this is not inferred or tested compatibility
- Static check
- 88 / 100 · heuristic scan, not runtime safety proof
- Author / version / license
- @aristoteleo · no license declared
- Fluxly token estimate
- Lean
- Fluxly setup estimate
- Plug-and-play
- External API key
- No requirement detected
- Detected OS requirements
- Unspecified
- Runtime requirements
- Unspecified
- Detected file/system behavior
-
- Read-only
- Detected network behavior
- Local-only
- Install commands
- None (reference only)
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。
The current SKILL.md does not define a fixed output example. 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,
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
# 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](./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
1. **Before analysis**: Scan this index for relevant skills
2. **Load skill file**: Read the full skill document for detailed guidance
3. **Follow best practices**: Use the code snippets and workflows provided
4. **Adapt as needed**: Skills are templates; adjust for your specific data Author text anchors workflow facts; Fluxly only indexes current sections, terms, files, and commands.
sections -> Cell & Nucleus Segmentation → Using Skills
terms -> Skill index · Skills · Cellpose · SAM-Based Methods · When to use · Before analysis · Load skill file · Follow best practices
files/cmd -> GPU/CPU · segmentation/SKILL.md · ./segmentation/SKILL.md · cell/nucleus
body sha256 -> 27edff33837e
Decide Fit First
Design Intent
How To Use It
Boundaries And Review