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| import streamlit as st | |
| import google.generativeai as genai | |
| from PIL import Image | |
| import os | |
| from dotenv import load_dotenv | |
| import PyPDF2 | |
| import io | |
| from datetime import datetime | |
| # Page configuration must be the first Streamlit command | |
| st.set_page_config( | |
| page_title="OCT Retina Analysis Assistant", | |
| page_icon="👁️", | |
| layout="wide", | |
| initial_sidebar_state="expanded" | |
| ) | |
| # Load environment variables | |
| load_dotenv() | |
| # Configure Gemini API | |
| genai.configure(api_key=os.getenv("GOOGLE_API_KEY")) | |
| model = genai.GenerativeModel("gemini-2.0-flash-exp") | |
| # Custom CSS | |
| st.markdown(""" | |
| <style> | |
| .main { | |
| padding: 2rem; | |
| } | |
| .stButton>button { | |
| width: 100%; | |
| background-color: #FF4B4B; | |
| color: white; | |
| padding: 0.5rem; | |
| margin-top: 1rem; | |
| } | |
| .credit-box { | |
| background-color: #f0f2f6; | |
| padding: 1rem; | |
| border-radius: 0.5rem; | |
| margin: 1rem 0; | |
| } | |
| .header-box { | |
| background-color: #FF4B4B; | |
| padding: 2rem; | |
| border-radius: 0.5rem; | |
| color: white; | |
| margin-bottom: 2rem; | |
| text-align: center; | |
| } | |
| .image-container { | |
| margin: 1rem 0; | |
| padding: 1rem; | |
| border-radius: 0.5rem; | |
| background-color: #f0f2f6; | |
| } | |
| .analysis-container { | |
| margin-top: 1rem; | |
| padding: 1rem; | |
| border-radius: 0.5rem; | |
| background-color: #f0f2f6; | |
| } | |
| </style> | |
| """, unsafe_allow_html=True) | |
| # System prompts | |
| SINGLE_TIMEPOINT_PROMPT = """You are an expert ophthalmologist specializing in interpreting macular Optical Coherence Tomography (OCT) scans. Your goal is to provide an accurate description and a possible diagnosis, supported by clear medical reasoning. These scans are from the same patient at a single timepoint. Please provide a comprehensive analysis. | |
| Step 1: Image Quality Assessment | |
| For each scan, describe the overall image quality, noting any artifacts or limitations that may affect your analysis. | |
| Step 2: Layer-by-Layer Analysis Across All Scans | |
| Analyze each of the retinal layers across all provided scans, describing: | |
| • Thickness patterns: Note any variations or consistencies in layer thickness | |
| • Morphological changes: Compare layer appearance across scans | |
| • Reflectivity patterns: Identify any recurring patterns or changes | |
| • Document abnormalities and their distribution across scans | |
| Step 3: Comprehensive Foveal Analysis | |
| Analyze the foveal region across all scans: | |
| • Compare foveal contour and thickness | |
| • Note any consistent or varying abnormalities | |
| • Identify patterns of foveal involvement | |
| Step 4: Integrated Abnormality Assessment | |
| Provide a unified analysis of abnormalities across all scans: | |
| • Distribution patterns | |
| • Progression or variation in appearance | |
| • Relationship between findings in different scans | |
| Step 5: Differential Diagnoses | |
| Based on the comprehensive analysis: | |
| • List potential diagnoses supported by findings across multiple scans | |
| • Explain how the pattern of findings supports each diagnosis | |
| • Note any temporal or spatial progression that helps narrow the diagnosis | |
| Step 6: Most Likely Diagnosis | |
| Provide a unified diagnosis considering all scans: | |
| • Explain how the combined findings support this diagnosis | |
| • Discuss any progression or pattern that confirms the diagnosis | |
| • Address any variations or inconsistencies | |
| Step 7: Recommendations | |
| Suggest: | |
| • Additional tests or imaging if needed | |
| • Follow-up scanning recommendations | |
| • Treatment considerations based on the comprehensive analysis""" | |
| COMPARISON_PROMPT = """You are an expert ophthalmologist specializing in interpreting macular Optical Coherence Tomography (OCT) scans. Your goal is to provide an accurate description and a possible diagnosis, supported by clear medical reasoning. These scans are from the same patient at two different timepoints. Please provide a comprehensive analysis and comparison. | |
| Step 1: Image Quality Assessment | |
| For each set of scans, describe the overall image quality, noting any artifacts or limitations that may affect your analysis. | |
| Step 2: Layer-by-Layer Comparison | |
| Compare the retinal layers between timepoints: | |
| • Changes in thickness patterns | |
| • Evolution of morphological features | |
| • Alterations in reflectivity patterns | |
| • Progression or regression of abnormalities | |
| Step 3: Foveal Evolution Analysis | |
| Compare the foveal region between timepoints: | |
| • Changes in contour and thickness | |
| • Evolution of abnormalities | |
| • Progression or improvement patterns | |
| Step 4: Disease Progression Assessment | |
| Analyze changes between timepoints: | |
| • Quantify and describe changes in abnormalities | |
| • Identify new or resolved findings | |
| • Assess overall disease progression or improvement | |
| Step 5: Treatment Response Evaluation | |
| If treatment was administered: | |
| • Evaluate effectiveness | |
| • Identify areas of improvement | |
| • Note resistant or worsening areas | |
| Step 6: Updated Diagnosis and Prognosis | |
| Based on the temporal comparison: | |
| • Confirm or revise previous diagnosis | |
| • Assess disease trajectory | |
| • Provide prognostic insights | |
| Step 7: Recommendations | |
| Suggest: | |
| • Treatment modifications if needed | |
| • Follow-up interval | |
| • Additional testing if required | |
| • Preventive measures""" | |
| TREATMENT_GUIDELINES_PROMPT = """Based on the current diagnosis and findings, please provide evidence-based treatment recommendations following established ophthalmological guidelines. Consider: | |
| 1. Standard of Care | |
| • First-line treatments | |
| • Alternative options | |
| • Contraindications | |
| 2. Treatment Plan | |
| • Immediate interventions | |
| • Long-term management | |
| • Follow-up schedule | |
| 3. Monitoring Parameters | |
| • Key metrics to track | |
| • Warning signs | |
| • Success indicators | |
| 4. Patient Education | |
| • Lifestyle modifications | |
| • Self-monitoring instructions | |
| • Prevention strategies""" | |
| def extract_pdf_text(pdf_file): | |
| """Extract text from uploaded PDF file""" | |
| pdf_reader = PyPDF2.PdfReader(pdf_file) | |
| text = "" | |
| for page in pdf_reader.pages: | |
| text += page.extract_text() | |
| return text | |
| def analyze_oct_images(images, timepoint=None, patient_data=None): | |
| """Analyze OCT images with optional timepoint and patient data""" | |
| if timepoint: | |
| prompt = f"{SINGLE_TIMEPOINT_PROMPT}\n\nTimepoint: {timepoint}\n" | |
| else: | |
| prompt = f"{SINGLE_TIMEPOINT_PROMPT}\n" | |
| if patient_data: | |
| prompt += f"\nPatient Information:\n{patient_data}\n" | |
| prompt += "\nPlease analyze these OCT scans:" | |
| content = [prompt] + images | |
| response = model.generate_content(content) | |
| return response.text | |
| def compare_oct_timepoints(images1, date1, images2, date2, patient_data=None): | |
| """Compare OCT images from two timepoints""" | |
| prompt = f"{COMPARISON_PROMPT}\n\nTimepoint 1: {date1}\nTimepoint 2: {date2}\n" | |
| if patient_data: | |
| prompt += f"\nPatient Information:\n{patient_data}\n" | |
| prompt += "\nPlease compare these OCT scans:" | |
| content = [prompt] + images1 + images2 | |
| response = model.generate_content(content) | |
| return response.text | |
| def get_treatment_recommendations(diagnosis, findings): | |
| """Get treatment recommendations based on guidelines""" | |
| prompt = f"{TREATMENT_GUIDELINES_PROMPT}\n\nDiagnosis: {diagnosis}\nFindings: {findings}" | |
| response = model.generate_content(prompt) | |
| return response.text | |
| def main(): | |
| # Header with custom styling | |
| st.markdown(""" | |
| <div class="header-box"> | |
| <h1>OCT Retina Analysis Assistant</h1> | |
| </div> | |
| """, unsafe_allow_html=True) | |
| # Credits | |
| st.markdown(""" | |
| <div class="credit-box"> | |
| <h3>About</h3> | |
| <p>Developed by Dr. Fernando Ly</p> | |
| <p>This tool assists in the analysis of OCT retina scans using advanced AI technology. | |
| It provides detailed layer analysis and potential diagnoses to support clinical decision-making.</p> | |
| <p><strong>Note:</strong> This tool is for assistance only and should not replace professional medical judgment.</p> | |
| </div> | |
| """, unsafe_allow_html=True) | |
| # Main content | |
| col1, col2 = st.columns([1, 1]) | |
| with col1: | |
| # Patient Data Section | |
| st.markdown("### Patient Information") | |
| patient_pdf = st.file_uploader("Upload Patient Data (PDF)", type=['pdf']) | |
| patient_data = None | |
| if patient_pdf: | |
| patient_data = extract_pdf_text(patient_pdf) | |
| with st.expander("View Patient Data"): | |
| st.text(patient_data) | |
| # Scan Upload Section | |
| st.markdown("### Upload OCT Scans") | |
| timepoint_option = st.radio( | |
| "Select scan type:", | |
| ["Single Timepoint", "Two Timepoints for Comparison"] | |
| ) | |
| if timepoint_option == "Single Timepoint": | |
| uploaded_files = st.file_uploader( | |
| "Choose OCT scans", | |
| type=['png', 'jpg', 'jpeg'], | |
| accept_multiple_files=True, | |
| key="single_timepoint" | |
| ) | |
| if uploaded_files: | |
| scan_date = st.date_input("Scan Date") | |
| st.markdown("### Uploaded Scans") | |
| images = [] | |
| for idx, uploaded_file in enumerate(uploaded_files): | |
| with st.expander(f"OCT Scan {idx + 1}", expanded=True): | |
| image = Image.open(uploaded_file) | |
| images.append(image) | |
| st.image(image, use_container_width=True, caption=f"OCT Scan {idx + 1}") | |
| if st.button("🔍 Analyze Scans"): | |
| with st.spinner("Analyzing OCT scans... Please wait."): | |
| try: | |
| analysis = analyze_oct_images(images, scan_date, patient_data) | |
| treatment_recs = get_treatment_recommendations( | |
| "Based on the analysis above", | |
| "See detailed findings above" | |
| ) | |
| with col2: | |
| st.markdown("### Analysis Results") | |
| st.markdown(f""" | |
| <div class="analysis-container"> | |
| {analysis.replace(chr(10), '<br>')} | |
| </div> | |
| """, unsafe_allow_html=True) | |
| st.markdown("### Treatment Recommendations") | |
| st.markdown(f""" | |
| <div class="analysis-container"> | |
| {treatment_recs.replace(chr(10), '<br>')} | |
| </div> | |
| """, unsafe_allow_html=True) | |
| except Exception as e: | |
| st.error(f"An error occurred during analysis: {str(e)}") | |
| else: # Two Timepoints | |
| st.markdown("#### First Timepoint") | |
| files1 = st.file_uploader( | |
| "Choose first set of OCT scans", | |
| type=['png', 'jpg', 'jpeg'], | |
| accept_multiple_files=True, | |
| key="timepoint1" | |
| ) | |
| date1 = st.date_input("First Scan Date") | |
| st.markdown("#### Second Timepoint") | |
| files2 = st.file_uploader( | |
| "Choose second set of OCT scans", | |
| type=['png', 'jpg', 'jpeg'], | |
| accept_multiple_files=True, | |
| key="timepoint2" | |
| ) | |
| date2 = st.date_input("Second Scan Date") | |
| if files1 and files2: | |
| st.markdown("### Uploaded Scans") | |
| images1 = [] | |
| images2 = [] | |
| st.markdown("#### First Timepoint Scans") | |
| for idx, uploaded_file in enumerate(files1): | |
| with st.expander(f"OCT Scan {idx + 1} - First Timepoint", expanded=False): | |
| image = Image.open(uploaded_file) | |
| images1.append(image) | |
| st.image(image, use_container_width=True) | |
| st.markdown("#### Second Timepoint Scans") | |
| for idx, uploaded_file in enumerate(files2): | |
| with st.expander(f"OCT Scan {idx + 1} - Second Timepoint", expanded=False): | |
| image = Image.open(uploaded_file) | |
| images2.append(image) | |
| st.image(image, use_container_width=True) | |
| if st.button("🔍 Compare Timepoints"): | |
| with st.spinner("Analyzing and comparing OCT scans... Please wait."): | |
| try: | |
| comparison = compare_oct_timepoints( | |
| images1, date1, | |
| images2, date2, | |
| patient_data | |
| ) | |
| treatment_recs = get_treatment_recommendations( | |
| "Based on the comparison above", | |
| "See detailed findings above" | |
| ) | |
| with col2: | |
| st.markdown("### Comparison Results") | |
| st.markdown(f""" | |
| <div class="analysis-container"> | |
| {comparison.replace(chr(10), '<br>')} | |
| </div> | |
| """, unsafe_allow_html=True) | |
| st.markdown("### Treatment Recommendations") | |
| st.markdown(f""" | |
| <div class="analysis-container"> | |
| {treatment_recs.replace(chr(10), '<br>')} | |
| </div> | |
| """, unsafe_allow_html=True) | |
| except Exception as e: | |
| st.error(f"An error occurred during analysis: {str(e)}") | |
| # Instructions in col2 if no files uploaded | |
| if not (patient_pdf or (timepoint_option == "Single Timepoint" and uploaded_files) or | |
| (timepoint_option == "Two Timepoints for Comparison" and files1 and files2)): | |
| with col2: | |
| st.markdown("### Instructions") | |
| st.markdown(""" | |
| 1. Upload patient data PDF (optional) | |
| 2. Choose analysis type (single timepoint or comparison) | |
| 3. Upload OCT scans for selected timepoint(s) | |
| 4. Set scan dates | |
| 5. Click analyze/compare button | |
| 6. Review analysis and treatment recommendations | |
| Supported formats: | |
| - Patient Data: PDF | |
| - OCT Scans: PNG, JPG, JPEG | |
| """) | |
| if __name__ == "__main__": | |
| main() |