AI-Powered 3D Cell Culture, Organoids & Biofabrication: From Scaffold Design to Drug Screening

Aim

Course Objectives

Syllabus

📅 Day 1: AI-Enhanced Scaffold Design and 3D Cell Culture Systems

Focus
Understanding the fundamentals of AI-assisted scaffold design and its role in creating biologically relevant 3D cell culture environments.

Topics Covered

• Introduction to 2D vs 3D cell culture models
• Why 3D culture models are more representative of in vivo environments
• AI-based scaffold material selection and optimization
• Designing porous scaffolds for tissue engineering applications

AI Tools / Practical Tools

• ChatGPT / Gemini: Scaffold design planning and material comparison
• Tinkercad: 3D design of scaffold structures
• OpenSCAD: Custom CAD tool for scaffold modeling
• Google Colab: Python-based tools for scaffold simulation and nutrient gradient modeling

Hands-on Session

1. AI-Assisted Scaffold Design: Participants will use AI prompts to compare scaffold materials like Matrigel, GelMA, and synthetic hydrogels for specific tissue applications.
2. Basic 3D Scaffold Design: Hands-on creation of a simple porous scaffold using Tinkercad or OpenSCAD, focusing on design principles such as pore size and geometry.

📅 Day 2: AI in Bioprinting, Organoids, and Microfluidic Systems

Focus
Exploring the role of AI in bioprinting, organoid creation, and microfluidic systems for dynamic 3D culture environments.

Topics Covered

• Introduction to 3D bioprinting and its applications in tissue engineering
• AI-assisted optimization of bioprinting parameters for scaffold fabrication
• Organoid creation: from stem cells to disease models
• Microfluidic systems for simulating tissue behavior and drug responses

AI Tools / Practical Tools

• Slic3r / UltiMaker Cura: 3D printing software for scaffold optimization
• LangChain + Streamlit: AI-driven optimization of bioprinting parameters
• Google Colab: Python-based simulations of perfusion in bioprinted scaffolds

Hands-on Session

1. Bioprinting Path Optimization: Participants will import scaffold designs and optimize them using Slic3r and Cura, focusing on print path, layer height, and pore geometry.
2. AI-Based Bioprinting Troubleshooting: Participants will use AI tools to diagnose and fix common bioprinting issues like nozzle clogging and shape fidelity.

📅 Day 3: AI-Powered Bioimage Analysis, Drug Screening, and Clinical Translation

Focus
Applying AI to analyze 3D cell culture images, predict drug responses, and understand the clinical applications of organoid models.

Topics Covered

• AI-based bioimage analysis: segmentation, organoid boundary detection, and morphological analysis
• Drug response modeling using organoids and spheroids
• Translating research findings into clinical applications: personalized medicine and precision oncology
• Clinical deployment of AI tools in drug discovery and patient-derived organoid testing

AI Tools / Practical Tools

• Fiji/ImageJ: AI-assisted microscopy image analysis
• Cellpose: AI-based cell segmentation tool
• DeepImageJ: Deep learning-based image segmentation
• Google Sheets / LibreOffice Calc: Analyzing drug response data and calculating IC50 values

Hands-on Session

1. AI-Powered Organoid Segmentation: Participants will segment and analyze organoid images using Fiji/ImageJ, Cellpose, or DeepImageJ.
2. 3D Dose-Response Analysis: Using drug response data, participants will calculate IC50 values and compare responses in 2D vs. 3D models.

Who Should Enrol?

Course Outcomes

Meet Your Mentor(s)

Prof. Kumud Malhotra

Professor & Dean

Prof. Kumud Malhotra, Dean of the University Institute of Physical and Life Sciences with 30 years of experience is an academician and administrator and has attained the highest echelons in the educational sector by managing senior positions, like Director, Dean, Managing Editor, or Editor-in-Chief . . . for content development and journal publication. She completed her Ph. D on “Genetic Epidemiology of Malaria in Some Population Groups of Delhi and Tribal Groups of Tarai Region of Nainital District” and Post Doctorate from Delhi University as an ICMR and UGC fellow.
Her expertise domains are Biotechnology, Genetics, Bioinformatics, Forensic  Science, Molecular Biology, and its allied areas. She has obtained Certifications in the areas of Genetic Engineering, Molecular Biology, Microarrays, Proteomics, and Parasitology from IGIB, NICD, MRC, and Delhi University. Down the lane, her achievements and accolades are the best employee and faculty while working at Bioinformatics Institute of India and RNB GLOBAL University as a Dean and other prestigious awards. Her contribution to the establishment of the School of Basic and Applied Sciences and Agricultural Sciences along with the approval from ICAR at the new University RNBGLOBAL
University was acknowledged by the Management.
Apart from teaching and academics her experience in content development and e-learning for various renowned universities and organizations like Banasthali Vidyapith, GOLS Academy, Biionline, etc. is an added credential of hers. Dr. Kumud Malhotra has been a Resource Person in Course Development Committees (for graduate and post-graduate programs) for Indira Gandhi National Open University (IGNOU), Jamia Hamdard along with other credits like Member of various committees like Academic Council, BOS, Research Committee, etc. for the IGNOU, IAMR. She has demonstrated caliber as a resourceful Technical Collaborator for the conduction of the Workshop on Bioinformatics at
Bundelkhand University and in Engineering College in Durg, Chhattisgarh with an appreciation letter from the university.
She is a member of the editorial board of various journals and has presented Papers at International Conferences on Genetics, Parasitology, Clinical Trials, Pharmacovigilance, Biotechnology, etc. Dr. Malhotra has delivered keynote addresses at CII, International Conferences, and member of various professional bodies Genetics Society, Indian Science Congress, International Society for Malariology and Parasitology, IAA, SBTI, etc. She has guided many students for Ph.D. and internships and got the projects from ICMR.