Sync template from atomicqms-style deployment

README.md

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-# pathology
+# Pathology & Laboratory Medicine Quality Management System
 
-A comprehensive QMS template designed for anatomic pathology, clinical pathology, and laboratory medicine departments.
+A comprehensive QMS template designed for anatomic pathology, clinical pathology, and laboratory medicine departments.
+
+## 🔬 Designed For
+
+- **Anatomic Pathology** - Surgical pathology, cytopathology, autopsy
+- **Clinical Pathology** - Chemistry, hematology, microbiology, transfusion medicine
+- **Reference Laboratories** - Specialized testing services
+- **Molecular Pathology** - Genetic and molecular diagnostics
+- **Forensic Pathology** - Medical examiner and coroner services
+- **Dermatopathology** - Skin biopsy interpretation
+- **Neuropathology** - Brain and nervous system pathology
+
+## 📋 Regulatory Framework
+
+This template supports compliance with:
+
+- **CAP** - College of American Pathologists accreditation
+- **CLIA** - Clinical Laboratory Improvement Amendments
+- **The Joint Commission** - Hospital accreditation (laboratory chapter)
+- **FDA** - IVD and LDT regulations
+- **AABB** - Blood bank standards (if applicable)
+- **State Clinical Laboratory Licensing** - State-specific requirements
+- **OSHA** - Bloodborne pathogens, chemical safety
+- **HIPAA** - Patient information privacy
+- **ASCP** - Pathologist and technologist standards
+- **CAP Biorepository** - Tissue banking requirements (if applicable)
+
+## Repository Structure
+
+```
+├── SOPs/
+│   ├── Specimen-Handling/     # Accessioning, processing, storage
+│   ├── Histology/             # Tissue processing, embedding, sectioning, staining
+│   ├── Cytology/              # Cytology preparation and screening
+│   ├── Autopsy/               # Post-mortem examination procedures
+│   ├── Molecular/             # Molecular testing, NGS, PCR
+│   └── General/               # Document control, training, CAPA
+├── Forms/
+│   ├── Requisition-Forms/     # Specimen submission, clinical history
+│   ├── Grossing-Templates/    # Specimen dictation templates
+│   ├── QC-Records/            # Staining QC, reagent logs, instrument checks
+│   ├── Report-Templates/      # Synoptic and narrative report templates
+│   ├── Competency/            # Technologist and pathologist assessments
+│   └── Incident-Reports/      # Specimen quality, labeling errors
+├── Policies/                  # Department policies
+├── Work-Instructions/         # Step-by-step procedures
+└── Templates/                 # Document templates
+```
+
+## Document Numbering Convention
+
+- **POL-XXX**: Policies
+- **SOP-SP-XXX**: Specimen Handling SOPs
+- **SOP-HIS-XXX**: Histology SOPs
+- **SOP-CYT-XXX**: Cytology SOPs
+- **SOP-AUT-XXX**: Autopsy SOPs
+- **SOP-MOL-XXX**: Molecular SOPs
+- **WI-XXX**: Work Instructions
+- **FRM-XXX**: Forms and Records
+
+## 🤖 AI-Powered Assistance
+
+This repository includes **AtomicAI**, your pathology QMS assistant. Mention `@atomicai` in any issue or pull request to:
+
+- Draft specimen handling and processing SOPs
+- Create histology and staining procedures
+- Generate grossing templates for specimen types
+- Develop molecular testing protocols
+- Create quality control procedures
+- Review documents for CAP/CLIA compliance
+
+### Example Prompts
+
+- "@atomicai create an SOP for surgical specimen grossing and sampling"
+- "@atomicai draft a tissue processor validation procedure"
+- "@atomicai write an immunohistochemistry staining and QC protocol"
+- "@atomicai create a synoptic report template for breast cancer"
+- "@atomicai develop a frozen section procedure with turnaround time standards"
+- "@atomicai create a specimen labeling and identification policy"
+
+## Getting Started
+
+1. **Establish Specimen Policies** - Define accessioning and handling requirements
+2. **Standardize Processing** - Document histology and cytology procedures
+3. **Implement QC Programs** - Set up staining, reagent, and instrument QC
+4. **Define Reporting Standards** - Create synoptic and narrative templates
+5. **Train Staff** - Use competency assessment forms
+
+## Key Documents to Create First
+
+1. **Specimen Accessioning SOP** - Receiving, labeling, and logging specimens
+2. **Tissue Processing SOP** - Fixation, processing, embedding procedures
+3. **H&E Staining Protocol** - Routine hematoxylin and eosin procedure
+4. **Immunohistochemistry SOP** - IHC staining and controls
+5. **Frozen Section SOP** - Intraoperative consultation procedure
+6. **Grossing Manual** - Specimen-specific grossing guidelines
+7. **Critical Values Policy** - Urgent result communication
+
+## Special Considerations for Pathology
+
+### Specimen Integrity
+- Specimen identification and labeling
+- Fixation timing and adequacy
+- Cold ischemia documentation
+- Tissue banking considerations
+- Chain of custody (legal cases)
+
+### Quality Control
+- H&E and special stain QC
+- IHC positive and negative controls
+- Reagent expiration and storage
+- Instrument calibration and maintenance
+- Proficiency testing participation
+
+### Reporting
+- Turnaround time standards
+- Synoptic reporting (CAP protocols)
+- Critical/unexpected results
+- Amendment and addendum procedures
+- Second opinion and consultation
+
+### Safety
+- Formalin handling and exposure limits
+- Xylene substitutes and ventilation
+- Infectious specimen handling
+- Sharps safety (microtome blades)
+- Prion precautions (CJD)
+
+---
+
+*This template is maintained by AtomicQMS. For questions, open an issue in this repository.*