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Introduction to 3D Tissue Mapping: April 28, 2021

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Marisa Lim edited this page Apr 28, 2021 · 1 revision

Introduction to 3D Tissue Mapping

When: April 28th, from 10:00 am-12:00 pm PDT

Instructors: Andreas Bueckle (abueckle@iu.edu, https://andreas-bueckle.com/), Ellen Quardokus (ellenmq@iu.edu)

Moderator: Saranya Canchi

Helpers: Abhijna Parigi, Marisa Lim, Jose Sanchez, Jeremy Walter, Elizabeth Record

Description: This free 2 hour hands-on workshop will introduce you to tools developed by the Human BioMolecular Atlas Program (HuBMAP) for mapping and registering tissue blocks and sections to 3-dimensional organ models with a Common Coordinate Framework (CCF) system. The workshop will introduce the Registration User Interface (RUI), the Exploration User Interface (EUI), and the Anatomical Structures,Cell Types and Biomarkers (ASCT+B) Tables and Visualization tool.

While we wait to get started --

  1. ✔️ Have you checked the pre-workshop resources page?

  2. 📝 Please fill out our pre-workshop survey if you have not already done so! Click here for survey link

  3. ✔️ Some useful videos on concepts covered today!

Introductions (20 minutes)

This workshop is a joint effort between the training and engagement team for the NIH Common Fund Data Ecosystem (CFDE) and the Common Fund supported Human BioMolecular Atlas Program (HuBMAP). CFDE is a project supported by the NIH to increase data reuse and cloud computing for biomedical research.

Goals for today:

  • learn about Common Coordinate Framework (CCF)
  • learn about Registration User Interface (RUI)
  • learn about Exploration User Interface (EUI)
  • learn about Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Tables

How to ask questions ?

If you have questions at any point:

  • Drop them in the chat, or
  • Direct messages to the moderator are welcome, or
  • Unmute yourself and ask during the workshop

We will be using the ✋ for non verbal communication to gauge participation during the hands-on activities.

Human BioMolecular Atlas Program (HuBMAP)

An overview of the HuBMAP consortium video

Consortium weblink: https://hubmapconsortium.org/#

It takes trillions of cells to build a human adult, and how those cells interact, connect, and arrange into tissues has a direct effect on our health. HuBMAP (the Human BioMolecular Atlas Program) will create the next generation of molecular analysis technologies and computational tools, enabling the generation of foundational 3D tissue maps and construction of an atlas of the function and relationships among cells in the human body. These maps and atlas can lead us to a better understanding of how the relationships among our cells affects our health.

Why Common Coordinate Framework (CCF) ?

What is it? CCF portal link: https://hubmapconsortium.github.io/ccf/index.html

Talk about the CCF Ontology

An overview on What is an Ontology? video

Go to https://hubmapconsortium.github.io/ccf/pages/ccf-ontology.html and show the connection between the different scales of data/ given organ

Instructor Switch !

Talk about CCF 3D Reference Object Library (10 minutes)

Go to https://hubmapconsortium.github.io/ccf/pages/ccf-3d-reference-library.html

Show the 3D reference objects for the 11 organs.

Babylon.js: https://sandbox.babylonjs.com/

Registration User Interface (RUI) (25 minutes)

The RUI can be used to register tissue blocks to the HuBMAP database or to learn about the 3-dimensional context of tissue blocks within organs.

go to https://hubmapconsortium.github.io/ccf-ui/rui/

RUI Usage SOP (point #2 under "Versions of the Registration User Interface" contains information how to use the tool as a non-HuBMAP user)

5 organs available now, with a total of 11 to be available around the end of May 2021 !

  • Large Intestine
  • Heart
  • Kidney (Left)
  • Kidney (Right)
  • Spleen

Each of the organs currently available in the RUI represent a ‘problem set’ of issues or commonalities with other organ systems.

We will demo the system by creating a tissue block to:

  • showcase the different views along with 3D view
  • create and download a JSON file
  • reload the downloaded file to bring up previously registered coordinates
  • share the workshop demo file to participants to use for ASCT+B tables demo

Hands-on activity (~15 minutes)

For any organ of choice, create a tissue block that encompasses at least three Anatomical Structural Tags and bisects one of the common extraction sites for that organ.

Note: Ensure to download the tissue blocks to use later for bonus exercise.

Exploration User Interface (15 minutes)

Overall Workflow:

  • Click on EUI
  • Highlight the different features:
    • Filters based on demography, Assays or Tissue Providers
    • Clicking on the indented list on the left gives overall summary for the organ. Clicking on the organ in the list, updates the data boxes on top and on right. However, you still see all the organs.
    • Clicking the organ in the indented list also preselects all the tissue blocks for that organ. Typically unselected tissue blocks are whitish changing to blue whne you hover over them or are selected. They all apprear blue if preselected and change to a light blue shade on hover or select.
    • Clicking on organ icon on top removes the organ from view in the 3D body model.
  • Use mouse scroll to zoom in and out and rotate the 3D bodies
    • Use this feature to rotate to posterior view and zoom in on kidney's in the female body
  • Showcase the multiple tissue blocks and the associated data
    • You can either click on the tissue block to select the data associated with it or check any data box to select a tissue block
    • Click on the block on right kidney (Male, Age 48, BMI 35.3) and look at donor and data files. Show the AF, PAS and MALDI images.
      • What wavelengths of light are emitted by the DAPI, eGFP and dsRed channels?
      • What is autofluorescence (AF) and how is it used?
      • Explain the Periodic Acid-Schiff (PAS) histology stained image
      • Explain what the different options are for channels in MALDI-IMS image; each "image" is composed of charge-to-mass ratios that can be translated into specific lipids via the LipidMAPs database.
    • Click on the block on left kidney and look at donor and data files.
      • showcase the use of filters to view specific assays (Female sex, and Assays --> PAS, AF, MALDI)
      • Select a block from left kidney (Female, Age 66, BMI 25.4) and show the different data images

EUI build with SPARC data: Link

Instructor Switch !

Anatomical Structure Mapping (20 minutes)

The underlying mapping of anatomical structures found in the RUI is defined by the Anatomical Structure, Cell Types and Biomarkers (ASCT+B) Tables.

Load the JSON file back into RUI (the workshop demo file based on Right kidney) and pull the Anatomical Structure Tags.

Go to the ASCT+B reporter, which is a web based visualization render of the tables: https://hubmapconsortium.github.io/ccf-asct-reporter/ and click on Visualization, scroll down and select "kidney"

  1. Search for renal medulla --> show all the related Functional Tissue Units (FTUs)
    • note this sub structure has no cell type and biomarker information
  2. Search for kidney capsule --> clicking on the node highlights the associated cell type and biomarkers which can be explored further
    • note Foxd1 is a Kidney specific Transcription Factor
  3. Select "indented list" from the toolbar--> explore the anatomical structures
  4. Select "report" from the toolbar--> save the report and open it in Excel to explore the details
  5. Select "data tables" from the toolbar (this brings you to the ASCT+B table used for the Reporter visualization)

Bonus hands-on activity

Exercise 1:

Upload the tissue block registration file you created in the hands-on activity. Pick any two Anatomical Structural Tags and explore them in the ASCT+B Reporter by selecting the appropriate organ. Do all of them have cell type and biomarker information ?

Exercise 2:

Compare your own data or data from a published paper for one of the organs with a v1 Master table (i.e. cell types with associated biomarkers). To do this, copy the column header format for cell types and for biomarkers and fill them in with your data; make the Google sheet publically shareable. Use the "Compare" feature to compare it to the Master tables?

Note how your data compares to what exists in the Master tables.

How can you engage with HuBMAP ?

Q&A

📝 Please fill out our post-workshop survey! We use the feedback to help improve our training materials and future workshops. Click here for survey link !

Questions?

Resources

The youtube videos are part of a larger playlist, click here to watch them all!

Check our FAQs and discussion board on tools and topics from this workshop and more!

Links for Moderator to share:

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