Application Guides
Each application guide organizes learning resources relevant to a specific application:
- Video tutorials and demonstrations
- Standard operating procedures
- Feature maps of applications
- Step-by-step guides to complete workflows
Available application guides listed alphabetically:
The Exploration User Interface (EUI) represents data across multiple scales, supporting navigation by multiple coordinate systems, including spatial, physiologic, and organ-based browsing. The first proof-of-concept user interface for the CCF v1.0.0 became available in June 2020. The EUI continues to evolve as more data becomes available. The EUI code is available on GitHub.
- EUI 1.7.0 Demo
- How to double-check a RUI registration with the EUI
- Tutorial: Using the Exploration User Interface (EUI) on the GTEx Portal
- Spatial Search in the Exploration User Interface
- Select Organ: One can navigate available organs by selecting them from the carousel above the stage or using the ontology on the left.
- Filter: Above the Search is the Filter icon which opens a flyout with many options (e.g. Sex, Assay Types, etc) for refining what tissue data is presented.
- Registered Blocks: It is possible to select a block of tissue samples either using the bodies on stage or the cards in the right column. Color coding helps to identify different selections.
- Data: Using the cards in the right column, click on items to dig deeper into the data.
- Start: Click the Add Spatial Search button.
- Select: Choose a donor sex and an organ to explore.
- Explore: Use the Probing Sphere to explore the organ in 3D Space by colliding with Tissue Blocks. Data updates on the left side menu as Tissue Block collisions are detected.
- Run Spatial Search: Click the Run Spatial Search button to use the Spatial Location results as a Filter. Add as many Spatial Searches as needed.
- Apply Filters: Click the Apply Filters button to analyze your Spatial Locations in the Exploration User Interface.
- Modify Spatial Locations: In the Filters area, Spatial Location results can be selected or deselected using the checkbox. Spatial Locations can be deleted by clicking the trash can icon. Click the Apply Filters button to analyze modified Spatial Locations in the Exploration User Interface.
- Movement Options:
- Keyboard: Use keys Q, A, W, S, D, and E to move the Probing Sphere.
- Mouse: Click a Tissue Block to center the Probing Sphere on the block.
- Resize: Increase or decrease the radius size of the Probing Sphere.
- Navigation Speed: Press Shift on the keyboard while pressing any navigation button to increase the navigation speed of the Probing Sphere.
- Zoom: Use the mouse wheel or trackpad to zoom in and out.
- Rotate: Modify the camera view by using the mouse or trackpad to click and drag in the desired direction.
- Reset: Click the Reset Camera View button or the Reset Probing Sphere button to start fresh.
The Registration User Interface (RUI) supports the registration of three-dimensional (3D) tissue blocks within 3D organ models. A first beta of the RUI became available in October 2020. Registration data is used in current versions of the Human Reference Atlas and the Exploration User Interface (EUI). The RUI code is available on GitHub.
- Enter author name and donor name to track data provenance.
- Select a reference organ.
- Select a set of common tissue extraction sites.
- Size the tissue block in three dimensions.
- Enter information on tissue section thickness.
- Position and rotate the 3D tissue block so that its placement correctly mirrors the tissue block extraction site.
- Identify anatomical structure tags via collision detection and manual annotation.
- Save all registration information into a file for easy uploading to custom templates in REDCap (or other systems) used to keep track of tissue and tissue registration data. If using the RUI integrated into the HuBMAP Ingestion Portal, registration information is automatically saved with the associated tissue block.