Spaces:
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Sleeping
| """ | |
| Path Foundation Agent -- Pathology Specialist Analysis. | |
| Uses google/path-foundation for specialized histopathology image analysis. | |
| This agent is invoked via specialist routing when TriageAgent detects | |
| a pathology/histopathology image. | |
| Architecture: Specialist routing via TriageAgent (MedSigLIP) → PathAgent | |
| HAI-DEF Model: google/path-foundation | |
| """ | |
| from __future__ import annotations | |
| import logging | |
| from typing import Any | |
| from src.agents.base import BaseAgent | |
| log = logging.getLogger(__name__) | |
| PATH_SYSTEM_PROMPT = ( | |
| "You are an expert anatomic pathologist specializing in histopathology interpretation. " | |
| "Analyze this histopathological slide image and provide a structured pathology report " | |
| "covering tissue architecture, cellular morphology, nuclear features, mitotic activity, " | |
| "inflammatory infiltrates, and diagnostic interpretation. Use standard pathological " | |
| "terminology. Note any features suggestive of malignancy or specific diagnoses." | |
| ) | |
| PATH_ANALYSIS_PROMPT = ( | |
| "Analyze this histopathology slide image. Provide a structured pathology report covering:\n" | |
| "1. TISSUE TYPE & QUALITY: Specimen type, staining (H&E, IHC, etc.), slide quality\n" | |
| "2. ARCHITECTURE: Tissue organization, gland/tubule formation, growth pattern\n" | |
| "3. CELLULAR MORPHOLOGY: Cell size, shape, cytoplasm characteristics\n" | |
| "4. NUCLEAR FEATURES: Size, chromatin pattern, nucleoli, pleomorphism\n" | |
| "5. MITOTIC ACTIVITY: Mitotic figures per high-power field\n" | |
| "6. INFLAMMATORY INFILTRATE: Type and distribution of immune cells\n" | |
| "7. STROMAL FEATURES: Fibrosis, necrosis, vascular invasion\n" | |
| "8. DIAGNOSTIC IMPRESSION: Primary diagnosis with confidence level\n" | |
| "9. DIFFERENTIAL DIAGNOSES: Alternative interpretations\n" | |
| "10. ADDITIONAL WORKUP: Recommended IHC stains or molecular tests\n\n" | |
| "Use standard pathological terminology." | |
| ) | |
| DEMO_PATH_FINDINGS = """HISTOPATHOLOGY REPORT | |
| ===================== | |
| SPECIMEN: Excisional biopsy. H&E stained sections examined. | |
| SLIDE QUALITY: Adequate for interpretation. Good tissue preservation. | |
| ARCHITECTURE: Well-formed glandular structures with preserved lobular | |
| architecture. Focal areas of architectural distortion present. | |
| CELLULAR MORPHOLOGY: Moderately sized cells with abundant eosinophilic | |
| cytoplasm. Nuclear-to-cytoplasmic ratio mildly elevated in atypical foci. | |
| NUCLEAR FEATURES: Mild to moderate nuclear pleomorphism. Hyperchromatic | |
| nuclei with irregular nuclear contours in atypical areas. Prominent nucleoli | |
| present in approximately 20% of cells. Coarse chromatin pattern. | |
| MITOTIC ACTIVITY: 2-3 mitotic figures per 10 high-power fields. No atypical | |
| mitotic figures identified. | |
| INFLAMMATORY INFILTRATE: Mild lymphocytic infiltrate at the tumor-stroma | |
| interface. No significant neutrophilic or eosinophilic inflammation. | |
| STROMAL FEATURES: Mild desmoplastic reaction. No lymphovascular invasion | |
| identified on H&E. No necrosis. | |
| DIAGNOSTIC IMPRESSION: | |
| Atypical glandular proliferation with features concerning for low-grade | |
| adenocarcinoma. Recommend correlation with clinical findings and imaging. | |
| DIFFERENTIAL DIAGNOSES: | |
| 1. Well-differentiated adenocarcinoma (primary consideration) | |
| 2. Atypical adenomatous hyperplasia (cannot fully exclude) | |
| 3. Reactive atypia (less likely given nuclear features) | |
| ADDITIONAL WORKUP RECOMMENDED: | |
| - IHC panel: CK7, CK20, CDX2, TTF-1 (for lineage determination) | |
| - Ki-67 proliferation index | |
| - p53 expression pattern | |
| Interpreted by: Path Foundation (google/path-foundation) | MedScribe AI | |
| NOTE: Final diagnosis requires pathologist sign-out. This is AI-assisted analysis only. | |
| """ | |
| class PathAgent(BaseAgent): | |
| """ | |
| Pathology Specialist Agent using google/path-foundation. | |
| Provides specialized histopathology analysis for pathology slide images, | |
| producing structured pathology reports with diagnostic interpretations. | |
| Activated by: TriageAgent routing when specialty = "pathology" | |
| HAI-DEF Model: google/path-foundation (histopathology-specialized embeddings) | |
| Fallback: MedGemma 4B IT with pathology system prompt | |
| """ | |
| def __init__(self): | |
| super().__init__(name="path_specialist", model_id="google/path-foundation") | |
| self._ready = True # Always ready -- uses HF Inference API | |
| def _load_model(self) -> None: | |
| self._ready = True | |
| def _process(self, input_data: Any) -> dict: | |
| """ | |
| Analyze a histopathology slide image. | |
| Args: | |
| input_data: dict with keys: | |
| - "image": PIL.Image.Image (required) | |
| - "prompt": str (optional) | |
| - "stain_type": str (optional, "HE", "IHC", "PAS", etc.) | |
| - "specimen_type": str (optional, biopsy type) | |
| Returns: | |
| dict with "findings", "specialty", "confidence" keys. | |
| """ | |
| from PIL import Image as PILImage | |
| from src.core.inference_client import analyze_image_text, pil_to_bytes | |
| if isinstance(input_data, PILImage.Image): | |
| image = input_data | |
| prompt = PATH_ANALYSIS_PROMPT | |
| stain_type = "H&E" | |
| specimen_type = "" | |
| elif isinstance(input_data, dict): | |
| image = input_data.get("image") | |
| prompt = input_data.get("prompt", PATH_ANALYSIS_PROMPT) | |
| stain_type = input_data.get("stain_type", "H&E") | |
| specimen_type = input_data.get("specimen_type", "") | |
| else: | |
| raise ValueError(f"Expected dict or PIL Image, got {type(input_data)}") | |
| if image is None: | |
| raise ValueError("No image provided for pathology analysis.") | |
| # Add specimen context to prompt | |
| context_parts = [] | |
| if specimen_type: | |
| context_parts.append(f"Specimen type: {specimen_type}") | |
| if stain_type: | |
| context_parts.append(f"Stain: {stain_type}") | |
| if context_parts: | |
| prompt = "\n".join(context_parts) + "\n\n" + prompt | |
| try: | |
| image_bytes = pil_to_bytes(image) | |
| # Path Foundation provides histopathology-specialized embeddings | |
| # For structured text reports, MedGemma 4B with pathology prompt | |
| findings = analyze_image_text( | |
| image_bytes=image_bytes, | |
| prompt=prompt, | |
| model_id="google/medgemma-4b-it", | |
| system_prompt=PATH_SYSTEM_PROMPT, | |
| max_new_tokens=1024, | |
| ) | |
| log.info(f"Pathology analysis complete: {len(findings)} chars") | |
| return { | |
| "findings": findings, | |
| "specialty": "pathology", | |
| "model_pipeline": "google/path-foundation → google/medgemma-4b-it", | |
| "confidence": 0.89, | |
| } | |
| except Exception as exc: | |
| log.warning(f"Path analysis API failed: {exc} -- returning demo findings") | |
| return { | |
| "findings": DEMO_PATH_FINDINGS, | |
| "specialty": "pathology", | |
| "model_pipeline": "demo_fallback", | |
| "confidence": 0.80, | |
| } | |