🦕 PaleoClaw

An AI Research Agent for Paleontology
古生物学 AI 研究助手

📢 What's New | 最新动态

🎉 v1.3.1 (2026-03-11) — Bug Fixes & Improvements | 错误修复与改进

📐 Morphometric Analysis | 形态测量学分析

• 64 landmarks (all semilandmarks) | 64 个地标点
• TPS/CSV/Excel/JSON export | 多格式导出
• Compatible with MorphoJ & geomorph | 兼容主流 GM 软件
• Pure Node.js, no Python deps | 纯 Node.js 实现
• Based on DeepMorph (Xiaokang Liu @ CUG) | 基于 DeepMorph

🖼️ Visualization | 可视化

• Landmark overlay images | 地标点标注图
• Before/after comparison | 处理前后对比
• Batch processing support | 批量处理支持

🔍 New CLI Commands | 新增命令

# Single image analysis | 单图像分析
paleoclaw agent --message "Extract landmarks from ammonoid.png"

# Batch processing | 批量处理
paleoclaw agent --message "Batch process specimens/ folder"

# Export formats | 导出格式
paleoclaw agent --message "Export as TPS for MorphoJ"

📊 Supported Fossils | 支持化石类型

• Ammonoids (菊石) | Brachiopods (腕足)
• Bivalves (双壳) | Gastropods (腹足)
• Trilobites (三叶虫) | Any clear silhouette

v1.2.0 (2026-03-09) — Profile Layers & Memory System | 个人画像与记忆系统

🧬 Profile Layers | 个人画像分层

• soul.md — System identity & principles | 系统身份与核心原则
• user.md — Personal research preferences | 个人研究偏好设置
• Double-layer personalization | 双层个性化架构

🧠 Memory System | 记忆系统

• Short-term & long-term memory | 短期与长期记忆
• Vector-based similarity search | 基于向量的相似度搜索
• Research trajectory tracking | 研究轨迹追踪

🔍 New CLI Commands | 新增命令

# Profile management | 画像管理
paleoclaw profile init    # Initialize | 初始化
paleoclaw profile show    # Display | 显示配置

# Memory management | 记忆管理
paleoclaw paleo-memory status     # Statistics | 状态统计
paleoclaw paleo-memory short      # Short-term | 短期记忆
paleoclaw paleo-memory long       # Long-term | 长期记忆
paleoclaw paleo-memory search     # Search | 内容搜索
paleoclaw paleo-memory archive    # Archive | 归档清理

v1.1.0 — Activity Monitoring | 活动监控

• 🖥️ Screen monitoring & screenshot capture | 屏幕监控与截图
• 📝 Activity logging (apps, files, websites) | 活动日志记录
• 📊 Daily productivity reports in Markdown | 每日生产力报告

v1.0.0 — Initial Release | 初始版本

• 📄 Paper search via CrossRef/Semantic Scholar/arXiv | 文献搜索
• 🦕 PBDB fossil occurrence queries | PBDB 化石记录查询
• 🧬 Taxonomic classification lookup | 分类学查询
• 📊 Stratigraphy & formation data | 地层学数据

🎯 Features | 功能特性

✨ Core Capabilities | 核心能力

Literature Search | 文献搜索

• CrossRef, Semantic Scholar, arXiv
• DOI validation & citation formatting
• Multi-source aggregation

Database Queries | 数据库查询

• PBDB fossil occurrences
• Taxonomic classifications
• Stratigraphic information

Bug Fixes & Improvements | 错误修复与改进 (v1.3.1+)

• 64 landmarks extraction
• TPS/CSV/Excel/JSON export
• MorphoJ & geomorph compatible
• Based on DeepMorph (Xiaokang Liu @ CUG)

AI-Powered Analysis | AI 分析

• Paper summarization
• Research synthesis
• Taxonomic verification

Memory System | 记忆系统

• Research history tracking
• Smart content retrieval
• Pattern recognition

Activity Monitoring | 活动监控

• Work session tracking
• Productivity metrics
• Daily log generation

Profile Customization | 个性化

• Research preference profiles
• Output format customization
• Workflow optimization

🚀 Quick Start | 快速开始

Prerequisites | 环境要求

| Requirement | Version | Description | |-------------|---------|-------------| | Node.js | >= 22.12.0 | Runtime environment | 运行环境 | | curl | latest | API calls | API 调用工具 | | Git | latest | Version control | 版本控制 |

Installation | 安装

# Install PaleoClaw | 安装 PaleoClaw
npm install -g paleoclaw@latest
# or | 或者
pnpm add -g paleoclaw@latest

# Initialize profile layers | 初始化个人画像
paleoclaw profile init

# Configure AI provider | 配置 AI 提供商
paleoclaw config set --ai-provider openai --ai-model gpt-5-mini

First Use | 首次使用

# Start the gateway | 启动网关
paleoclaw gateway --port 18789 --verbose

# Example queries | 示例查询
paleoclaw agent --message "Find papers about Jurassic theropods"
paleoclaw agent --message "Query PBDB for Tyrannosaurus occurrences"
paleoclaw agent --message "What is the classification of Velociraptor?"

📋 Usage Examples | 使用示例

🔍 Literature Search | 文献搜索

Command | 命令:

paleoclaw agent --message "Find papers about dinosaur extinction at K-Pg boundary from 2020-2026"

Output | 输出:

📄 Research Papers Found | 找到的研究论文:

1. The last dinosaurs: K-Pg boundary extinction patterns
   最后恐龙的灭绝：K-Pg 边界灭绝模式
   ├─ Authors: Smith, J., Johnson, K., Williams, R.
   ├─ Year: 2023
   ├─ Journal: Paleobiology
   ├─ DOI: 10.1016/j.palaeo.2023.111234
   └─ Citations: 42

2. Iridium anomalies and dinosaur extinction
   铱异常与恐龙灭绝
   ├─ Authors: Chen, L., et al.
   ├─ Year: 2022
   ├─ Journal: Cretaceous Research
   ├─ DOI: 10.1016/j.cretres.2022.105234
   └─ Citations: 28

🧬 Taxonomy Lookup | 分类学查询

Command | 命令:

paleoclaw agent --message "What is the full classification of Velociraptor mongoliensis?"

Output | 输出:

🦕 Taxonomic Classification | 分类学信息

Name | 名称: Velociraptor mongoliensis
Rank | 等级: species | 种
Status | 状态: valid | 有效

Full Hierarchy | 完整分类层级:
└─ Kingdom | 界: Animalia | 动物界
   └─ Phylum | 门: Chordata | 脊索动物门
      └─ Class | 纲: Dinosauria | 恐龙纲
         └─ Order | 目: Saurischia | 蜥臀目
            └─ Suborder | 亚目: Theropoda | 兽脚亚目
               └─ Family | 科: Dromaeosauridae | 驰龙科
                  └─ Genus | 属: Velociraptor | 伶盗龙属
                     └─ Species | 种: V. mongoliensis | 蒙古伶盗龙

Data source | 数据来源: Paleobiology Database (queried 2026-03-09)

🗺️ Fossil Occurrences | 化石记录

Command | 命令:

paleoclaw agent --message "Where have Tyrannosaurus fossils been found? Query PBDB."

Output | 输出:

🗺️ Fossil Occurrences for Tyrannosaurus | 霸王龙化石记录

📍 Location 1 | 地点 1: Montana, USA | 美国蒙大拿州
   ├─ Coordinates | 坐标: 45.0, -110.0
   ├─ Age | 年代: 66 Ma | 6600万年前
   └─ Formation | 地层: Hell Creek Formation | 地狱溪组

📍 Location 2 | 地点 2: South Dakota, USA | 美国南达科他州
   ├─ Coordinates | 坐标: 43.5, -102.5
   ├─ Age | 年代: 66 Ma
   └─ Formation | 地层: Hell Creek Formation

📍 Location 3 | 地点 3: Wyoming, USA | 美国怀俄明州
   ├─ Coordinates | 坐标: 44.0, -107.0
   ├─ Age | 年代: 66 Ma
   └─ Formation | 地层: Lance Formation | 兰斯组

📊 Total occurrences | 总记录数: ~50
🔗 Data source | 数据来源: PBDB (paleobiodb.org)

🏔️ Stratigraphy Query | 地层查询

Command | 命令:

paleoclaw agent --message "What is the age and location of Yixian Formation?"

Output | 输出:

🏔️ Stratigraphic Information | 地层信息

Formation | 地层名称: Yixian Formation | 义县组
Age | 年代: ~125 Ma | 约1.25亿年前
Period | 纪: Early Cretaceous | 早白垩世
Epoch | 世: Barremian-Aptian | 巴列姆期-阿普特期
Location | 地点: Liaoning, China | 中国辽宁
Lithology | 岩性: Volcaniclastic sediments | 火山碎屑沉积

🦕 Associated Fossils | 相关化石:
• Sinosauropteryx prima — First feathered dinosaur | 第一种带羽毛恐龙
• Confuciusornis sanctus — Early bird | 早期鸟类
• Psittacosaurus lujiatunensis — Ceratopsian | 鹦鹉嘴龙

⭐ Significance | 重要性: Lagerstätte with exceptional preservation
              具有 exceptional 保存状态的化石库

📐 Bug Fixes & Improvements | 错误修复与改进 (v1.3.1+)

Command | 命令:

paleoclaw agent --message "Extract landmarks from ammonoid.png"

Output | 输出:

📐 Morphometric Analysis Results | 形态测量分析结果

Specimen | 标本: ammonoid
Image Size | 图像尺寸: 512 x 512 pixels

Landmarks Detected | 检测到的地标点:
├─ 64 Landmarks (all semilandmarks) | 64 个地标点（全部为半地标点）
│  ├─ #1 LM1: (256, 128)
│  ├─ #2 LM2: (260, 130)
│  ├─ ... (62 more)
│  └─ #64 LM64: (255, 129)

Export Files | 导出文件:
├─ 📄 TPS: data/outputs/morphometrics/tps/ammonoid.tps
├─ 📊 CSV: data/outputs/morphometrics/csv/ammonoid.csv
├─ 📝 JSON: data/outputs/morphometrics/json/ammonoid.json
└─ 🖼️ Visualization: data/outputs/morphometrics/visualizations/ammonoid_landmarks.png

Compatible with | 兼容软件: MorphoJ, R geomorph, TPSdig
Based on | 基于: DeepMorph by Xiaokang Liu @ CUG

Batch Processing | 批量处理:

paleoclaw agent --message "Batch process all images in specimens/ folder"

Output | 输出:

📦 Batch Processing Complete | 批量处理完成

Total specimens | 总标本数: 25
Successfully processed | 成功处理: 23
Failed | 失败: 2

Results saved to | 结果保存至: data/outputs/morphometrics/
├─ tps/batch_results.tps
├─ csv/batch_results.csv
├─ json/batch_results.json
└─ visualizations/

Time elapsed | 耗时: 12.5 seconds

🔧 Configuration | 配置

Environment Variables | 环境变量

# AI Provider Configuration | AI 提供商配置
export PALEOCLAW_AI_PROVIDER=openai
export PALEOCLAW_AI_MODEL=gpt-5-mini
export PALEOCLAW_AI_API_KEY=your-api-key

# Alternative Providers | 其他提供商
export PALEOCLAW_AI_PROVIDER=qwen
export PALEOCLAW_AI_MODEL=qwen-plus-latest

# Profile Paths | 画像文件路径
export PALEOCLAW_SOUL_PATH=/path/to/soul.md
export PALEOCLAW_USER_PATH=/path/to/user.md

Config File | 配置文件

Location | 位置: ~/.paleoclaw/paleoclaw.json

{
  "agent": {
    "model": "openai/gpt-5-mini",
    "language": "zh-CN"
  },
  "skills": {
    "load": {
      "extraDirs": ["~/.paleoclaw/skills"]
    }
  },
  "memory": {
    "autoArchive": true,
    "archiveAfterDays": 7
  }
}

📁 Project Structure | 项目结构

PaleoClaw/
├── 📂 agents/                    # Agent configurations | 代理配置
│   └── paleoclaw-research-agent/
│       └── AGENT.md
├── 📂 skills/                    # Research skills | 研究技能
│   ├── 📄 paper_search/          # Literature search | 文献搜索
│   ├── 🦕 pbdb_query/            # Fossil database | 化石数据库
│   ├── 🧬 taxonomy_lookup/       # Taxonomy | 分类学
│   ├── 📊 stratigraphy_lookup/   # Stratigraphy | 地层学
│   ├── 📐 bug_fixes_improvements/ # Bug fixes & improvements | 错误修复与改进 (v1.3.1+)
│   ├── 64 landmarks (all semilandmarks) | 64 个地标点（全部为半地标点）
│   └── Based on DeepMorph by Xiaokang Liu @ CUG | 基于 DeepMorph
├── 📝 paper_summary/         # Paper summarization | 论文摘要
├── 🎯 research_assistant/    # Research workflow | 研究工作流
├── 🖥️ screen_monitor/        # Screen monitoring | 屏幕监控
├── 📝 activity_logger/       # Activity logging | 活动记录
└── 📊 daily_log_generator/   # Daily reports | 日报生成
├── 📂 src/paleoclaw/             # Core modules (v1.3.1+) | 核心模块
│   ├── 📂 profile/               # Profile system | 画像系统
│   │   ├── layers.ts             # Profile parser | 画像解析器
│   │   └── index.ts
│   ├── 📂 memory/                # Memory system | 记忆系统
│   │   ├── store.ts              # Memory storage | 记忆存储
│   │   ├── retrieval.ts          # Vector search | 向量搜索
│   │   └── index.ts
│   ├── 📂 cli/                   # CLI commands | 命令行接口
│   │   ├── profile-cli.ts        # Profile commands | 画像命令
│   │   ├── memory-cli.ts         # Memory commands | 记忆命令
│   │   └── index.ts
│   └── index.ts
├── 📂 docs/                      # Documentation | 文档
├── 📂 scripts/                   # Utility scripts | 工具脚本
├── 📄 soul.md                    # System identity | 系统身份
├── 📄 user.md                    # User preferences | 用户偏好
├── 📄 PALEOCLAW_IDENTITY.md      # Core system prompt | 核心系统提示
├── 📄 CHANGELOG.md               # Version history | 版本历史
├── 📄 UPGRADE_GUIDE_v1.2.0.md    # Upgrade guide | 升级指南
├── 📄 v1.2.0_CHECKLIST.md        # Release checklist | 发布检查清单
├── 📄 package.json
├── 📄 README.md
└── 📄 LICENSE

🔬 Scientific Integrity | 科学诚信

✅ Our Commitment | 我们的承诺

🔍 No Fabrication 不编造数据

All data verified against primary sources 所有数据均经过原始来源验证

📚 Verifiable Citations 可验证引用

Every paper includes valid DOI 每篇论文都包含有效 DOI

⚠️ Transparent Uncertainty 透明的不确定性

Clearly marks disputed data 清楚标记有争议的数据

🔄 Reproducible 可复现

Documents all queries and parameters 记录所有查询和参数

Data Verification Standards | 数据验证标准

1. Taxonomic names verified via PBDB | 分类学名称通过 PBDB 验证
2. Paper citations include valid DOI | 论文引用包含有效 DOI
3. Age ranges include uncertainty (in Ma) | 年代范围包含不确定性（百万年）
4. Disputed claims clearly marked | 有争议的声明清楚标记
5. Data sources explicitly cited | 数据来源明确引用

Handling Unknown Data | 处理未知数据

When data is unavailable | 当数据不可用时:

⚠️ No verified fossil occurrences found in PBDB for [taxon name].
   在 PBDB 中未找到 [分类群名称] 的已验证化石记录。

This may indicate | 这可能表明:
• Limited fossil record | 化石记录有限
• Recent taxonomic revision | 最近的分类学修订
• Data not yet in database | 数据尚未录入数据库

Recommendation | 建议: Check primary literature for recent discoveries.
              查阅原始文献以获取最新发现。

📚 Documentation | 文档

| Document | Description | 描述 | |----------|-------------|------| | USAGE_EXAMPLES.md | Detailed usage guide | 详细使用指南 | | INTEGRATION.md | Channel integration guide | 渠道集成指南 | | DEVELOPMENT.md | Contributor guide | 贡献者指南 | | PALEOCLAW_IDENTITY.md | Core system prompt | 核心系统提示 | | CHANGELOG.md | Version history | 版本历史 | | UPGRADE_GUIDE_v1.2.0.md | Upgrade instructions | 升级说明 |

🤝 Contributing | 贡献

We welcome contributions! Areas of interest | 我们欢迎贡献！感兴趣的领域：

• 🌍 New data source integrations | 新数据源集成
• 🔧 Additional research skills | 额外的研究技能
• 📝 Improved citation formatting | 改进的引用格式
• 🌐 Non-English language support | 非英语语言支持
• 📖 Documentation improvements | 文档改进

How to Contribute | 如何贡献

1. Fork the repository | Fork 仓库
2. Create a feature branch | 创建功能分支
3. Make your changes | 进行更改
4. Run tests: bash scripts/test.sh | 运行测试
5. Submit a pull request | 提交 Pull Request

📜 License | 许可证

MIT License — see LICENSE file for details.

🙏 Acknowledgments | 致谢

| Data Source | Provider | Description | |-------------|----------|-------------| | 🦕 PBDB | Paleobiology Database | Fossil occurrences & taxonomy | 化石记录与分类学 | | 📚 CrossRef | CrossRef | Literature metadata | 文献元数据 | | 📊 Semantic Scholar | Semantic Scholar | Citation analysis | 引用分析 | | 📝 arXiv | arXiv | Preprints | 预印本 | | 📐 DeepMorph | Xiaokang Liu @ CUG | Morphometric algorithms | 形态测量算法 |

📖 Citation | 引用

If you use PaleoClaw in your research, please cite | 如果您在研究中使用 PaleoClaw，请引用：

@software{paleoclaw2026,
  author = {PaleoClaw Contributors},
  title = {PaleoClaw: An AI Research Agent for Paleontology},
  year = {2026},
  url = {https://github.com/syxscott/PaleoClaw}
}

Data Source | 数据来源:

Paleobiology Database (PBDB): https://paleobiodb.org/

🔗 Support & Community | 支持与社区

| Channel | Link | Description | |---------|------|-------------| | 🐛 Issues | GitHub Issues | Bug reports & feature requests | 错误报告与功能请求 | | 💬 Discussions | GitHub Discussions | Community Q&A | 社区问答 | | 📖 Documentation | GitHub Docs | Full documentation | 完整文档 |

🦕 PaleoClaw: An AI Assistant for Paleontological Research

🦕 PaleoClaw：古生物学研究的 AI 助手