Sudha Gopalakrishnan Brain Centre

Indian Institute of Technology Madras
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Neuroanatomy Histology Laboratory

Brain Centre, is a unique facility in India that has a fully technology-driven histology pipeline for whole brain processing into digital data with process informatics fully embedded, all integrated environment-controlled facility.

Nissl Staining for cell bodies in the adult human cerebellum

Brain Centre, is a unique facility in India that has a fully technology-driven histology pipeline for whole brain processing into digital data with process informatics fully embedded, all integrated environment-controlled facility.

Myelin Silver impregnation for fibre tracts in the adult human cerebral cortex.

Brain Centre, is a unique facility in India that has a fully technology-driven histology pipeline for whole brain processing into digital data with process informatics fully embedded, all integrated environment-controlled facility.

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.
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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.
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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.
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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.
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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.
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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.
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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).

Publications

"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.

"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

"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.

"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.

"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). (Accepted for publication)

"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). (Accepted for publication)