Sudha Gopalakrishnan Brain Centre

Indian Institute of Technology Madras
HOME PEOPLE HIGHLIGHTS DATA PORTAL NEWS & EVENTS CAREER GALLERY CONTACTS
Whole humanbrain neuro mapping at cellular resolution
Nissl Staining for cell bodies in the adult human cerebellum
Myelin Silver impregnation for fibre tracts in the adult human cerebral cortex.

Brain Freezing

    Technology platform for freezing large brains in stereotaxic coordinates with minimal tissue damage or artifacts.

Slot Die Coater

    Automated system for application of 10-20μm thin adhesive layer on glass slides to preserve tissue integrity during tape transfer cryo-sectioning

Automated Tissue Transfer

    An automated system for cryo-sectioning and transfer of tissue to glass slides with minimal tissue damage.

Block Face Imaging

    An intermediate step in histopathology pipeline to detect structure and volume changes of the brain using imaging.

UV curing station

    Hands-free, tool-free method of transferring a 20-micron thick sectioned tissue onto a glass slide via controlled UV exposure

Large Format Autostainer

    A custom-built automated staining system for tissues mounted on multiformat slides (6x8, 5x7, 2x3, and 1x3) with uniformity and consistency.

Large format coverslipper (6x8)

    An automated system for uniform, bubble-free cover slipping operation of (6x8)slides with a throughput of 30 slides/hour.

Automated Coverslipper (2x3)

    A fully automated system capable of cover slipping (2x3) slides with a high throughput of 50 slides/hour.

Monitoring Dashboard

    Monitors critical operations in the lab - environmental parameters (temperature, humidity), coverslipping & staining. Generates reports and alerts users during failure

Scanning station

    Custom whole slide scanners for digitizing multi format slides at 0.5 μm/pixel resolution - developed in collaboration with an indigenous company.

Zero Foot Print Viewer

  • A tool to view Mircroscopically scanned image at a very high resolution.
  • Slices of brain of thickness 20microns scanned at a minimum size of 0.5microns is displayed using a viewer without the loss of any resolution or quality.
  • Tools Used: AngularJs, Django, Ng Gallery, Openlayers, IIP Server.
View the application

Atlas Creator

  • A tool used to draw annotations on the Microscopic High Resolution Image.
  • The regions of the brain needs to marked after viewing in the viewer. This tool is helpful to draw multiple geometry based annotations using particular regions, save, display and transfer between multiple users.
  • Tools Used: AngularJs, Django, Openlayers, IIP Server, GeoJSON.
View the application

Cell Annotation Tool

  • A tool used to paint on images at a pixel size.
  • The cells in the brain can be detected using Machine Learning Algorithms and to make it work better Manual Annotation is very useful. This can be achieved by this tool, drawing the cells at the pixel resolution.
  • Tools Used: AngularJs, Django, Openlayers, IIP Server, Konva.
View the application

3D Visualizer

  • A 3D visualizer is a tool that is used to create and display three-dimensional brain images.
  • These images can provide detailed information about the brain's structure and function, and can be used for a variety of purposes such as research, diagnosis, and surgical planning.
  • Tools Used: AngularJs, Django, threejs, IIP Server.
View the application

Registration (Manual & Automatic)

  • Image registration is a technique that is used to align multiple images from different imaging modalities, time points, or patients to a common coordinate system.
  • Image registration can be used to align preoperative images with real-time intraoperative images, which can help in the precise localization of surgical targets.
  • Tools Used: AngularJs, Django, Openlayers, IIP Server, Konva.
View the application

Series Viewer

  • Series viewers can be used to analyze large sets of images and identify patterns or trends.
  • Series viewers allow medical professionals to manipulate and analyze the images, which can be crucial for diagnosis and treatment planning.
  • Tools Used: AngularJs, Django, Openlayers, IIP Server, Konva.
View the application

Journals

Predictive modeling of Alzheimer's disease progression: Integrating temporal clinical factors and outcomes in time series forecasting

    K.H. Aqil , Prashanth Dumpuri , Keerthi Ram, Mohanasankar Sivaprakasam

     Intelligence-Based Medicine Volume 10, 2024, 100159 doi: 10.1016/j.ibmed.2024.100159

Systematic development of immunohistochemistry protocol for large cryosections-specific to non-perfused fetal brain

     Karthika Pandurangan , Jaikishan Jayakumar , Stephen Savoia , Reetuparna Nanda , S. Lata , E. Harish Kumar , Suresh S. , Sudha Vasudevan , Chitra Srinivasan , Jayaraj Joseph, Mohanasankar Sivaprakasam, Richa Verma

     J Neurosci Methods. 2024 May:405:110085. doi: 10.1016/j.jneumeth.2024.110085.

Histological characterization and development of mesial surface sulci in the human brain at 13–15 gestational weeks through high-resolution histology

    Richa Verma, Jaikishan Jayakumar, Rebecca Folkerth, Paul R. Manger, Mihail Bota, Moitrayee Majumder, Karthika Pandurangan, Stephen Savoia, Srinivasa Karthik, Ramdayalan Kumarasami, Jayaraj Joseph, G. Rohini, Sudha Vasudevan, Chitra Srinivasan, S. Lata, E. Harish Kumar, Rajeswaran Rangasami, Jayaraman Kumutha, S. Suresh, Goran Šimić, Partha P Mitra, Mohanasankar Sivaprakasam

     J Comp Neurol. 2024 Apr;532(4):e25612. doi: 10.1002/cne.25612.

Publications

Ano-swinMAE: Unsupervised Anomaly Detection in Brain MRI using swin Transformer based Masked Auto Encoder

    Kumari Rashmi, Ayantika Das, Naga Gayathri Matcha, Keerthi Ram, Mohanasankar Sivaprakasam

     MIDL 2024

Registration Quality Evaluation Metric with Self-Supervised Siamese Networks

    Tanvi Kulkarni, Sriprabha Ramanarayanan, Keerthi Ram , Mohanasankar Sivaprakasam

     MIDL 2024

Optimization of Freezing Method to Facilitate Cryosectioning of Large Brain Tissues

     Ramdayalan Kumarasami, Sathish Pandidurai, Srinivasa Karthik, Mohanasankar Sivaprakasam, Jayaraj Joseph

     2024 IEEE International Symposium on Medical Measurements and Applications (MeMeA) doi: 10.1109/MeMeA60663.2024.10596795

Blogs

Advancing Neuroscience Research with Visual Question Answering and Multimodal Retrieval

     Pralaypati Ta, Sriram Venkatesaperumal, Mohanasankar Sivaprakasam, Amit Kumar and Vega Shah

     Technical Blog , nvidia.Developer

Patents

Automated Coverslipper for Large Format Slides with Switchable Compatibility to Handle Multi Format Slides.

     Jayaraj Joseph, Mohanasankar Sivaprakasam, Jayaraman Kiruthi Vasan, Ramdayalan K, Rahul Manoj, and Sudhan Chandrasekaran

     WO 2023/275894, Jan. 5, 2023, Assigned to Indian Institute of Technology (IIT Madras).

Journals

A Standardized Protocol for the Safe Retrieval of Infectious Postmortem Human Brain for Studying Whole-Brain Pathology

    James RI, Verma R, Johnson LR, Manesh A, Jayakumar J, Sen M, Joseph J, Kumarasami R, Mitra PP, Sivaprakasam M, Varghese GM

     Am J Forensic Med Pathol. 2023 Jul 25. doi: 10.1097/PAF.0000000000000871. Epub ahead of print. PMID: 37490584.

A technology platform for standardized cryoprotection and freezing of large-volume brain tissues for high-resolution histology

     Ramdayalan Kumarasami , Richa Verma , Karthika Pandurangan , Jivitha Jyothi Ramesh, Sathish Pandidurai, Stephen Savoia, Jaikishan Jayakumar , Mihail Bota , Partha Mitra, Jayaraj Joseph , Mohanasankar Sivaprakasam

     Front. Neuroanat., 02 November 2023 Volume 17 - 2023 doi: 10.3389/fnana.2023.1292655

Wide field block face imaging using deep ultraviolet induced autofluorescence of the human brain

     Karthik, S., Joseph, J., Jayakumar, J., Manoj, R., Shetty, M., Bota, M., Verma, R., Mitra, P., & Sivaprakasam, M. (2023)

     Journal of Neuroscience Methods, 109921. https://doi.org/10.1016/j.jneumeth.2023.109921

Publications

Automation of slide staining for large tissue sections

     Prabhakar Sithambaram, Ramdayalan Kumarasami, Sathish Pandidurai, Selvadurai Sekar, Jayaraman Kiruthi Vasan, Mohanasankar Sivaprakasam, Jayaraj Joseph,

     2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Automation of slide coverslipping for large tissue sections

     Hari Narayanan, Sudhan Chandrasekaran, Jayaraman Kiruthi Vasan, Ramdayalan Kumarasami, Mohansankar Sivaprakasam, Jayaraj Joseph

     Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Image Quality Assessment of Large Tissue Samples Stained using a Customized Automated Slide Stainer

     P. Sithambaram, R. Kumarasami, M. Sivaprakasam and J. Joseph

     2023 IEEE International Symposium on Medical Measurements and Applications (MeMeA), Jeju, Korea, Republic of, 2023, pp. 1-6, doi: 10.1109/MeMeA57477.2023.10171900

Cover slip handling and mounting media dispensation for reliable automated cover slipping of large tissue sections

     H. Narayanan, S. Chandrasekaran, J. K. Vasan, R. Kumarasami, M. Sivaprakasam and J. Joseph

     2023 IEEE International Symposium on Medical Measurements and Applications (MeMeA), Jeju, Korea, Republic of, 2023, pp. 1-6, doi: 10.1109/MeMeA57477.2023.10171950.

Learning to atlas register for rapid segmentation of brain structures in fetal MRI

    Tanvi Kulkarni, Aqil K. H., Jaikishan Jayakumar, Keerthi Ram, Mohanasankar Sivaprakasam

     Volume 12464, Medical Imaging 2023: Image Processing; 124643V (2023) doi: 10.1117/12.2653953

A Study of Representational Properties of Unsupervised Anomaly Detection in Brain MRI

    Ayantika Das, Arun Palla, Keerthi Ram, Mohanasankar Sivaprakasam

     MICCAI 2023 workshop - Medical applications with disentanglements doi: 10.1007/978-3-031-25046-0_9

Confounding Factors Mitigation in Brain Age Prediction Using MRI with Deformation Fields

    K. H. Aqil, Tanvi Kulkarni, Jaikishan Jayakumar, Keerthi Ram, Mohanasankar Sivaprakasam

     MICCAI 2023 workshop - International Workshop on PRedictive Intelligence In MEdicine

Blogs

Whole Human Brain Neuro-Mapping at Cellular Resolution on NVIDIA DGX

     Keerthi Ram, Mohanasankar Sivaprakasam and Amit Kumar

     Technical Blog , nvidia.Developer

Publications

Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder–decoder deep networks.

    Samik Banerjee, Lucas Magee, Dingkang Wang, Xu Li, Bing-Xing Huo, Jaikishan Jayakumar, Katherine Matho, Meng-Kuan Lin, Keerthi Ram, Mohanasankar Sivaprakasam, Josh Huang, Yusu Wang, Partha P Mitra

     A reusable neural network pipeline for unidirectional fiber segmentation. Fioravante de Siqueira A, Ushizima DM, van der Walt SJ. Sci Data. 2022 Feb 2;9(1):32. doi: 10.1038/s41597-022-01119-6.