DATA

The following data types have been incorporated into the Atlas Spatial Viewer:

The data available in the Spatial Viewer are routinely added as they are generated and quality checked. A summary of the data available in the Spatial Viewer can be found on the Kidney Tissue Atlas homepage.

The spatial images presented in the application have been pre-processed in order to convert them to OME (Open Microscopy Environment) TIFF (tagged image file format) using Bio-Formats bftools version 5.8.

Each dataset is identified by a sample ID, which is derived from a segment of a participant's biopsy tissue. Every sample ID may be traced back to a single participant ID.

NAVIGATION

The Atlas Spatial Viewer allows you to search the available KPMP spatial datasets by data-level and participant-level attributes and visualize the associated datasets.

Figure: Spatial Viewer home page

DATASET LIST

Filter panel

Narrowing your search to a focused selection of datasets is accomplished using the filter panel on the left-hand side of the screen. The filter panel is divided in two tabs, DATASET and PARTICIPANT, with each tab containing  attributes by which to filter the dataset list to the right of the filter panel.

Participant-level filters allow searching for datasets that contain particular participant-level attributes such as age range, tissue type, etc. Dataset-level filters allow a user to search for different types of datasets (Light Microscopy vs 3D Cytometry).

To open a dataset in the viewer, click on the link in the SAMPLE ID column.

Sorting and resizing columns

Click on a column heading to sort the data in the column ascending order. Click on the column header a second time to sort in descending order.

When hovering over the column heading you will see a blue line that appears at the right hand side of the column. Click and drag the blue line to increase or decrease the column width.

Showing/hiding columns

By default the dataset list will display the SAMPLE ID, DATA TYPE, and IMAGE TYPE columns. Click the left button at the top of the dataset list and a field chooser will appear which allows you show additional columns or hide the active columns. NOTE: The SAMPLE ID column cannot be hidden.

VISUALIZATIONS

The Spatial Viewer uses the Vitessce visualization platform as its visualization engine. The layout and features/functionality of the visualization page will be specific to the data type selected.

Light Microscopic Whole Slide Images

Figure: Visualization page showing a Light Microscopic Whole Slide Image dataset

Data Set panel

The Data Set panel on the left displays information on the selected image, including a reiteration of the type of the selected dataset (e.g. “RGB max projection of 8-channel immunofluorescence image volume.”) The Data Set panel also contains additional image information such as X and Y dimension, pixel size, number of channels, etc.

Spatial panel

In the Spatial pane, you can zoom in and out of the image by using the scroll wheel on a mouse or with a trackpad. To download the current image, click on the download icon in the upper-right corner of the Spatial panel.

3D Tissue Imaging and Cytometry

Figure: Visualization page showing a 3D Tissue Imaging and Cytometry dataset

Spatial Layers

For images with multiple channels, a Spatial Layers panel will appear under the Data Set panel. This panel allows you to control which channels appear, designate channel colors, adjust the z axis, and set the opacity of the image.

Spatial Transcriptomics

Figure: Visualization page showing a Spatial Transcriptomics dataset

Expression Levels / Expression Histogram

Search for a gene of interest, select it, and the normalized expression level and corresponding number of cells will be graphed below in the Expression Histogram panel.

Spatial panel

The Spatial panel produces a heatmap showing the expression level for the selected gene on the various points on the tissue sample.

Scatterplot (UMAP) panel

Displays a scatterplot showing gene expression clusters and expression level for the selected gene as a heatmap.  

Atlas Spatial Viewer

Heading 1

Heading 2

The rich text element allows you to create and format headings, paragraphs, blockquotes, images, and video all in one place instead of having to add and format them individually. Just double-click and easily create content.

Static and dynamic content editing

A rich text element can be used with static or dynamic content. For static content, just drop it into any page and begin editing. For dynamic content, add a rich text field to any collection and then connect a rich text element to that field in the settings panel. Voila!

How to customize formatting for each rich text

Headings, paragraphs, blockquotes, figures, images, and figure captions can all be styled after a class is added to the rich text element using the "When inside of" nested selector system.

This is a link

Heading 3

The rich text element allows you to create and format headings, paragraphs, blockquotes, images, and video all in one place instead of having to add and format them individually. Just double-click and easily create content.

What’s a Rich Text element?

The rich text element allows you to create and format headings, paragraphs, blockquotes, images, and video all in one place instead of having to add and format them individually. Just double-click and easily create content.

Static and dynamic content editing

A rich text element can be used with static or dynamic content. For static content, just drop it into any page and begin editing. For dynamic content, add a rich text field to any collection and then connect a rich text element to that field in the settings panel. Voila!

How to customize formatting for each rich text

Headings, paragraphs, blockquotes, figures, images, and figure captions can all be styled after a class is added to the rich text element using the "When inside of" nested selector system.

Data

The following data types have been incorporated into the Atlas Explorer:

  • Single-nucleus RNA-seq
  • Single-cell RNA-seq
  • Regional transcriptomics

Participants in Atlas Explorer for each data type

A summary of the data available in the Atlas Explorer is available on the Kidney Tissue Atlas homepage.

The single-nucleus and single-cell datasets are described in detail in this preprint (Note: the v1.0 Atlas Explorer includes only a subset of the samples described); the manuscript also details the approach to assigning cell types to the clustered data.

The cell types noted in the application were established as a joint effort with the HuBMAP Consortium. The HuBMAP ASCT+B Reporter tool can be used to visualize the  anatomical structures, cell types, and biomarkers (ASCT+B) authored by the domain experts. The cell types and anatomical structures are also being represented in the Cell Ontology and Uberon, respectively.

Navigation

The Atlas Explorer allows users to search by genes, cell types, or supported technologies and see the associated data.

Gene Search

Searching for a gene presents the user with various visualizations and data tables displaying how the gene is expressed in the selected data type.

Choosing the single-nucleus or single-cell RNA-seq data types yields a visualization page with a "reference UMAP" showing how the full dataset was clustered as well as the inferred cell type/state of each cluster (see this preprint for more details on the clustering and cell attribution methods); a feature plot showing the expression of the selected gene, and a table detailing the expression of the selected gene in each cluster (compared to all other clusters) (Figure 1). Users can also filter the dataset down to only include AKI, CKD, or healthy reference samples - this updates the gene feature plot and the table (but not the reference UMAP image).

Figure 1: Navigating the Atlas Explorer visualization page

Searching for a gene and choosing the regional transcriptomics data type yields a visualization page with a "bubble plot" showing the expression of the selected gene across all tissue types (AKI, CKD, and healthy reference tissue) and microdissected regions, and a table detailing the expression of the selected gene in each region compared to all other regions (Figure 2). Users can also filter the dataset down to only include AKI, CKD, or healthy reference samples.

Figure 2: Regional transcriptomics visualization page

Cell Type Search

Users can also begin their search with a cell type instead of a gene. After searching for a cell type or selecting one from the renal corpuscle or nephron schemata (Figure 3), a user can see all of the data currently mapped to that cell type. As of Atlas Explorer v1.0, the available data will be single-nucleus and single-cell clusters or microdissected regions. After choosing one of the clusters/regions, users are presented with a table showing which genes are most differentially expressed in the selected cluster/region.

Figure 3: Cell type search (Tubules tab)

Atlas Explorer

Data

The Atlas Repository provides access to the datasets being generated by KPMP. The datasets available in the repository are a combination of raw and processed data from KPMP participant biopsies and reference tissue samples. Datasets are routinely added as they are generated and QCed. Some data files shown in the repository are "controlled access", meaning they can only be retrieved after a data use agreement is in place between KPMP and your organization. A summary of the data available in the repository is available on the Kidney Tissue Atlas homepage.

Navigation

Users can search for datasets using the filter panel on the left-hand side of the screen. There are two different facets available for searching and filtering: by Participants and by Files.

 Navigating the Atlas Repository

Participant-level filters allow a user to search for files that contain particular participants or participants with various attributes (e.g. sample type, tissue type). File-level filters allow a user to search for different types of files, such as certain file formats or experiment types.

Atlas Repository

DATA

The following data types have been incorporated into the Atlas Spatial Viewer:

The data available in the Spatial Viewer are routinely added as they are generated and quality checked. A summary of the data available in the Spatial Viewer can be found on the Kidney Tissue Atlas homepage.

The spatial images presented in the application have been pre-processed in order to convert them to OME (Open Microscopy Environment) TIFF (tagged image file format) using Bio-Formats bftools version 5.8.

Each dataset is identified by a sample ID, which is derived from a segment of a participant's biopsy tissue. Every sample ID may be traced back to a single participant ID.

NAVIGATION

The Atlas Spatial Viewer allows you to search the available KPMP spatial datasets by data-level and participant-level attributes and visualize the associated datasets.

Figure: Spatial Viewer home page

DATASET LIST

Filter panel

Narrowing your search to a focused selection of datasets is accomplished using the filter panel on the left-hand side of the screen. The filter panel is divided in two tabs, DATASET and PARTICIPANT, with each tab containing  attributes by which to filter the dataset list to the right of the filter panel.

Participant-level filters allow searching for datasets that contain particular participant-level attributes such as age range, tissue type, etc. Dataset-level filters allow a user to search for different types of datasets (Light Microscopy vs 3D Cytometry).

To open a dataset in the viewer, click on the link in the SAMPLE ID column.

Sorting and resizing columns

Click on a column heading to sort the data in the column ascending order. Click on the column header a second time to sort in descending order.

When hovering over the column heading you will see a blue line that appears at the right hand side of the column. Click and drag the blue line to increase or decrease the column width.

Showing/hiding columns

By default the dataset list will display the SAMPLE ID, DATA TYPE, and IMAGE TYPE columns. Click the left button at the top of the dataset list and a field chooser will appear which allows you show additional columns or hide the active columns. NOTE: The SAMPLE ID column cannot be hidden.

VISUALIZATIONS

The Spatial Viewer uses the Vitessce visualization platform as its visualization engine. The layout and features/functionality of the visualization page will be specific to the data type selected.

Light Microscopic Whole Slide Images

Figure: Visualization page showing a Light Microscopic Whole Slide Image dataset

Data Set panel

The Data Set panel on the left displays information on the selected image, including a reiteration of the type of the selected dataset (e.g. “RGB max projection of 8-channel immunofluorescence image volume.”) The Data Set panel also contains additional image information such as X and Y dimension, pixel size, number of channels, etc.

Spatial panel

In the Spatial pane, you can zoom in and out of the image by using the scroll wheel on a mouse or with a trackpad. To download the current image, click on the download icon in the upper-right corner of the Spatial panel.

3D Tissue Imaging and Cytometry

Figure: Visualization page showing a 3D Tissue Imaging and Cytometry dataset

Spatial Layers

For images with multiple channels, a Spatial Layers panel will appear under the Data Set panel. This panel allows you to control which channels appear, designate channel colors, adjust the z axis, and set the opacity of the image.

Spatial Transcriptomics

Figure: Visualization page showing a Spatial Transcriptomics dataset

Expression Levels / Expression Histogram

Search for a gene of interest, select it, and the normalized expression level and corresponding number of cells will be graphed below in the Expression Histogram panel.

Spatial panel

The Spatial panel produces a heatmap showing the expression level for the selected gene on the various points on the tissue sample.

Scatterplot (UMAP) panel

Displays a scatterplot showing gene expression clusters and expression level for the selected gene as a heatmap.  

Atlas Spatial Viewer

The KPMP Data Visualization Center (DVC) has developed a variety of internal and external applications to support the gathering, integration, and display of the data generated through this project. All software is freely accessible from our KPMP GitHub page.

Source Code