How to use the Atlas

Atlas Release Notes

TL;DR:

What’s new in each release of the Kidney Tissue Atlas ecosystem.

Atlas Ecosystem Releases

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AUGUST 2026 EXPLORER RELEASE HIGHLIGHTS

This month, we are publishing an off-cycle release to the Kidney Tissue Atlas to address a data classification correction affecting a subset of participants. During routine data quality review, we identified 15 participants whose Enrollment Category was incorrectly displayed as CKD (Chronic Kidney Disease). These participants should have been classified as AKI (Acute Kidney Injury). The corrected participant classifications are included in this off-cycle release. Participants 30-11260 and 30-11272 had available whole slide images, no other imaging, molecular, biomarker, or pathology data are currently available for any impacted participants.

In addition to this correction, we have introduced a new Adjudication Category: "DM-R - no histologic abnormalities". Participants assigned to this category were previously classified as "Other". This update provides greater clarity by identifying these participants as a distinct adjudication group within the Atlas.

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SAMPLE DETAILS AVAILABLE IN THE DATA CHANGE LOG

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Q2 2026 KIDNEY TISSUE ATLAS RELEASE

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Q2 2026 (v22) EXPLORER RELEASE HIGHLIGHTS

The nephron schematic images in the Atlas Explorer have been upgraded to feature detailed illustrations provided by the Human Reference Atlas. These enhanced visuals offer greater clarity in representing the structure and location of glomerular and tubular cell types. This update reflects our continuing efforts to provide more accurate, informative, and user-friendly resources for the research community.

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Additional improvements have been made to our Regional Transcriptomics differential expression tables and their functionality. Gene results are now clearer, with the addition of a comparison column and enhanced gene name hyperlinks that link directly to the relevant comparison, rather than just the overall results page. 

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Q2 2026 (v22) REPOSITORY AND SPATIAL VIEWER IMPROVEMENTS

We are in the process of updating our filtering to help users better understand how our data is organized and help them get to the information most relevant to defining what they need in the Atlas. 

Our first update in this area was to combine the Multimodal Imaging Mass Spectrometry (MALDI-IMS) with the Spatial Lipidomics filter. Now all Spatial Lipidomics data types are under one filter but are differentiated by their Platform.

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Based on user feedback, we have adjusted the order of elements within the “Dataset metadata” section to provide a more logical sequence for filtering. In the coming months, we will reach out for additional suggestions as we continue to improve the filtering organization and labeling of our available technologies. Thank you to everyone who has provided feedback: we regularly review and assess user suggestions to make the KPMP Atlas a more user-friendly source of information and data access.

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Lastly, we incorporated functionality allowing users to right click and  open Spatial Viewer images in new tabs. With the addition of this feature, users will be able to take advantage of a feature in Chrome allowing the ability to view two tabs side-by-side. 

View video for instructions Using Chrome to view images side-by-side

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Q2 2026 (v22) REPOSITORY AND SPATIAL VIEWER DATA RELEASE

*Data has been replaced and renamed as a newer version (file name ending in v2, v3, etc.). For details of what has been replaced and how to find updates, please see the Data Change Log

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*Data has been replaced and renamed as a newer version (file name ending in v2, v3, etc.). For details of what has been replaced and how to find updates, please see the Data Change Log.

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Q1 2026 KIDNEY TISSUE ATLAS RELEASE

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Q1 2026 (v21) EXPLORER RELEASE HIGHLIGHTS

  • Addressed duplicate gene results on Regional Transcriptomics Differential Expression page and provided clarity about which comparison set (Glom vs TI or All Regions) the gene appears in. 

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Q1 2026 (v21) REPOSITORY RELEASE HIGHLIGHTS

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Q1 2026 (v21) SPATIAL VIEWER RELEASE HIGHLIGHTS

  • See the Atlas Data Change Log regarding any updates/changes to existing data.
  • Minor improvements have been made for some visualizations:
    • Moved all navigation to the left side for a consistent experience.
    • The Multimodal Imaging Mass Cytometry visualization has been adjusted to provide a similar experience to METASPACE Lipidomics visualizations.

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Q4 2025 KIDNEY TISSUE ATLAS RELEASE

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Q4 2025 (v20) EXPLORER RELEASE HIGHLIGHTS

  • Addressed bug fixes related to Gene Expression Comparison across Cell Clusters tables not appearing for single-cell/single-nucleus RNAseq

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Q4 2025 (v20) REPOSITORY RELEASE HIGHLIGHTS

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Q4 2025 (v20) SPATIAL VIEWER RELEASE HIGHLIGHTS

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Q3 2025 KIDNEY TISSUE ATLAS RELEASE

The Q3 2025 Release of the Kidney Tissue Atlas marks a pivotal moment in our ongoing research endeavors. This highly anticipated release brings groundbreaking updates to our Atlas Explorer and unveils critical new data enhancements within the Atlas Repository.

The Atlas Explorer updates for both Single-cell RNA-seq and Single-nucleus RNA-seq set the stage for the upcoming publication, “Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney,”, which is now accessible on bioRxiv. This update introduces additional samples and novel cell types, promising to deepen our understanding of kidney disease. More information about associated data can be found in the KPMP Collections page https://doi.org/10.48698/16dd-vj20. KPMP data for this publication may be found in the Atlas Repository by filtering to Dataset metadata/DOIs/10.48698/16dd-vj20. 

Importantly, the Atlas Repository now offers Whole Genome Sequence data, available to researchers with a completed Data Use Agreement. A publicly available comprehensive documentation package accompanies this data, providing KPMP participant IDs, file mapping, process guidelines, and quality assurance protocols.

The summaries below offer a snapshot of the remarkable contributions made by our participant heroes, their recruitment sites, and the research laboratories generating the data, highlighting the collective efforts of our entire consortium in advancing kidney disease research.

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Q3 2025 (v19) EXPLORER RELEASE HIGHLIGHTS

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Q3 2025 (v19) REPOSITORY RELEASE HIGHLIGHTS

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Q3 2025 (v19) SPATIAL VIEWER RELEASE HIGHLIGHTS

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Q2 2025 KIDNEY TISSUE ATLAS RELEASE

The KPMP is pleased to announce the Q2 2025 Release of the Kidney Tissue Atlas. The 2022 baseline central laboratory data is being re-released (Plasma Serum Biomarker Data-BC AU5812-2022.v2). This release also includes a wealth of additional biomarker data available from plasma, urine, and stool biospecimens.

The summaries below outline the data in this release, highlighting both the impact in terms of file counts and the participants who contributed to each data type this quarter.

Q2 2025 (v18) SPATIAL VIEWER RELEASE HIGHLIGHTS

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Q2 2025 (v18) REPOSITORY RELEASE HIGHLIGHTS

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Q1 2025 (v17) RELEASE HIGHLIGHTS

Data released to the Atlas Repository (1,912):

  • 10X Multiome (63)
    • ATAC-seq (42)
    • Single-nucleus RNAseq (35)
  • 3D Tissue Imaging Cytometry (261)
  • Biomarker Data (2)
    • Metabolon Plasma/Serum (1)
    • Metabolon Urine (1)
  • Clinical (1)
  • CODEX (32)
  • Light Microscopy Whole Slide Images (681)
  • Multimodal Imaging Mass Spectrometry (88)
  • Pathology Descriptor Scoring (1)
  • Single-cell RNAseq (255)
  • Spatial Transcriptomics (514)

Data released to the Atlas Spatial Viewer (586):

  • CODEX (8)
  • Light Microscopy Whole Slide Images (520)
  • Multimodal Imaging Mass Spectrometry (58)

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Q4 2024 (v16) RELEASE HIGHLIGHTS

Software updates:

Experience the improved filtering features in Repository and Spatial Viewer!‍
The filters panel layout was redesigned and the filter options were expanded, empowering you to effortlessly select data based on attributes from the KPMP publicly available clinical data file.

Now you can easily select data tailored to your specific interests like Primary Adjudicated Category, Baseline eGFR, Diabetes Duration, A1c, and more! Dive in and experience the power of this enhanced functionality:

Video Demo of Updates

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Data released to the Atlas Repository (874):

  • 10X Multiome (75)
    • ATAQ-seq (42)
    • Single-nucleus RNAseq (47)
  • Clinical Data (1)
  • CODEX (136)
  • CUT&RUN (207)
  • Imaging Mass Cytometry (78)
  • Light Microscopy Whole Slide Images (252)
  • Multimodal Molecular Imaging (40)
  • Single-cell RNAseq (25)
  • Spatial Lipidomics (6)
  • Spatial Metabolomics (40)

Data released to the Atlas Spatial Viewer (446):

  • CODEX (34)
  • Imaging Mass Cytometry (124)
  • Light Microscopy Whole Slide Images (185)
  • Spatial Lipidomics (23)
  • Spatial Metabolomics (80)

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Q3 2024 (v15) RELEASE HIGHLIGHTS

Data released to the Atlas Repository (1,008):

  • 10X Multiome (203)
    • ATAQ-seq (126)
    • Single-nucleus RNAseq (103)
  • Clinical Data (1)
  • CODEX (24)
  • Pathology Descriptor Scoring (1)
  • Light Microscopy Whole Slide Images (307)
  • Segmentation Masks & Pathomics Vectors (updated) (222)
  • Single-cell RNAseq (224)

Data released to the Atlas Spatial Viewer (455):

  • CODEX (6)
  • Light Microscopy Whole Slide Images (227)
  • Segmentation Masks & Pathomics Vectors (222)

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Q2 2024 (v14) RELEASE HIGHLIGHTS

Data released to the Atlas Repository (1,277):

  • 10X Multiome (17)
  • ATAQ-seq (193)
  • Single-nucleus RNAseq (137)
  • Clinical Data (1)
  • CODEX (44)
  • CUT & RUN (99)
  • Spatial Lipidomics (38)
  • Spatial Metabolomics (42)
  • Light Microscopy Whole Slide Images (706)

Data released to the Atlas Spatial Viewer (790):

  • CODEX (11)
  • Spatial Lipidomics (151)
  • Spatial Metabolomics (84)
  • Light Microscopy Whole Slide Images (544)

Review the Data Change Log for details of specific data changes to any of the Atlas applications.

Software Updates:

  • The available data tables on the Atlas home page and the Atlas Explorer home page now include a ALL count of available samples/files.
  • The single-cell and single-nucleus RNAseq data now link out to both v1.0 and v1.5 in CELLXGENE.
  • Review the Known Issues Tracker for details of specific functionality issues, fixes, and workarounds related to functionality in the Atlas.
  • We continue to make minor fixes to our applications that will improve our users’ experience and the security of our data and applications.

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‍Q1 2024 (v13.0)

Data released to the Atlas Explorer (2):

  • Single-cell RNA-seq v1.5 (79 samples from 77 participants)
  • Single-nucleus RNA-seq v1.5 (80 participants)

Note: these datasets will also be available in CELLxGENE in early April 2024

Data released to the Atlas Repository (388):

  • 3D Tissue Imaging and Cytometry (63)
  • Clinical Data (1)
  • CODEX (104)
  • Imaging Mass Cytometry (60)
  • Single-cell RNA-seq v1.5 (1)
  • Single-nucleus RNA-seq v1.5 (1)
  • Spatial Lipidomics (2)
  • Spatial Metabolomics (48)
  • Spatial N-glycomics (16)
  • Whole Slide Images (91)

Data released to the Atlas Spatial Viewer (413):

  • 3D Tissue Imaging and Cytometry (115)
  • CODEX (26)
  • Imaging Mass Cytometry (77)
  • Spatial Lipidomics (10)
  • Spatial Metabolomics (96)
  • Spatial N-glycomics (17)
  • Light Microscopy Whole Slide Images (72)

Software Updates:

  • Overall
    • Minor cosmetic changes have been incorporated across the Atlas.
    • “Enrollment Category” has replaced the term “Tissue Type” when referring to enrollment disease cohorts  AKI, CKD, DM-R, and Healthy Reference. This change is intended to more easily differentiate how participants are categorized at enrollment in the KPMP study and categorized after the KPMP adjudication process.
    • Review the Known Issues Tracker for details of specific functionality issues, fixes, and workarounds.
    • Review the Data Change Log for details of specific data changes to any of the Atlas applications.
  • Explorer
    • Links to CELLxGENE for v1.0 and v1.5 of both Single-cell and Single-nucleus RNA-seq data
    • Link to GitHub for Single-nucleus RNA-seq pipelines
    • Adjusted p-value has been corrected in the Differential Expression tables for Regional Transcriptomics
    • Minor fixes for clarity of content
  • Atlas Repository
    • Minor display enhancements

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February 2024

Data released to the Atlas Repository (3):

  • Primary Adjudicated Category
  • SomaScan Plasma Proteomics
  • SomaScan Urine Proteomics

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December 2023 (v12.0)

‍Data released to the Atlas Repository (972):

  • Whole Slide Images (382)
  • 3D Tissue Imaging and Cytometry (297)
  • 10X Multiome (197) (note that there is some overlap among these files)
  • ATAC-Seq (132)
  • Single-nucleus RNA-Seq (107)
  • Spatial Transcriptomics (39)
  • Spatial Lipidomics (11)
  • Spatial N-glycomics (2)
  • Regional Proteomics aggregated analysis package (1)
  • Clinical Data (1)

Data released to the Atlas Spatial Viewer (642):

  • Light Microscopy Whole Slide Images (430)
  • 3D Tissue Imaging and Cytometry (165)
  • Spatial Lipidomics (44)
  • Spatial N-glycomics (3)

Software Updates:

  • Explorer Regional Proteomics - The Beta visualization of the Regional Proteomics data is now available in the Atlas Explorer. More features will be available for this data type in Q1 2024. 
  • Help menu - We have updated our Help menu in the upper right of the Atlas to show more detail of what resources are available to users.
  • Spatial Viewer - We have updated the Spatial Viewer to the most current version of Vitessce.

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October 2023 (v11.0)

Data released to the Atlas Repository (1,721):

  • 10X Multiome (193) (note that there is some overlap among these files)
  • ATAC-Seq (132)
  • Single-nucleus RNA-Seq (99)
  • CUT & RUN (143)
  • Descriptor Scoring (1)
  • DNA Methyl-seq (120)
  • Single-cell RNA-Seq (50)
  • Biomarker Data: Stool Microbiome Metagenomics (2)
  • Regional Proteomics aggregated data package (1)
  • Whole Slide Images (579)
  • Segmentation Data (222)
  • Spatial Lipidomics (34)
  • Spatial N-glycomics (18)
  • Spatial Transcriptomics (319)
  • Clinical Data (1)

Data released to the Atlas Spatial Viewer (615):

  • Light Microscopy Whole Slide Images (422)
  • Spatial Lipidomics (129)
  • Spatial N-glycomics (24)
  • Spatial Transcriptomics (40)

Software Updates:

  • Repository Participant Information page - This panel, originally featured in the Spatial Viewer and containing participant-specific information (e.g. disease, age, eGFR), is now available in the Atlas Repository with even more information.
  • Spatial Viewer Recently Released - In the Spatial Viewer users may now click on the “Recently Released” check box on the File tab to select only those files that are new or updated in the current release.
  • Explorer formatting updates - 
  • Explorer now has a more clearly defined access to CellXGene for users looking for disease-specific differential expression analysis of the KPMP data.
  • The format of the gene expression tables has been updated for easier reading

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June 2023 (v10.0)

‍New publications and their associated DOIs:

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Data released to the Atlas Repository:

  • Single-cell RNA-Seq (50)
  • Regional Proteomics (118)
  • 10X Multiome (188) (note that there is some overlap among these files)
  • ATAC-Seq (123)
  • Single-nucleus RNA-Seq (99)
  • Whole Slide Images (80)
  • Opportunity Pool Biomarker Data:
  • Plasma Biomarker Data-BC AU5812-2022 (1)
  • Urine Biomarker Data-BC AU5812-2022 (includes timed urine information) (1)
  • Urine Biomarker Data-UHPLC MS_MS-2022 (includes timed urine information) (1)
  • Plasma Biomarker Data-UHPLC MS_MS-2022 ) (1)
  • Urine Biomarker Data-BC AU680-2022 (includes timed urine information) (1)
  • Spatial Lipidomics (corrected metadata spreadsheet) (1)
  • Updated open access clinical data file (includes DM-R) (1)

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Data released to the Atlas Spatial Viewer:

  • Light Microscopy Whole Slide Images (80)
  • Spatial Lipidomics (corrected link) (1)

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Software Updates:

  • Atlas Repository UI - The Atlas Repository user interface has been updated for consistency across Atlas applications and to allow for future enhancements.
  • CSV download - Filter the files you want and create a complete list of the files in a CSV. This will be helpful when making data requests or requesting DOIs be minted and associated with publications. The current CSV file is limited to 1000 rows due to technical issues we will resolve in Q3.
  • Diabetes Mellitus - Resilient (DM-R) - The tissue type of “Diabetic Nephropathy Resistor”, which was introduced in Q1 2023 has been relabeled to “Diabetes Mellitus - Resilient” (DM-R) to better reflect this participant group. As you may recall, these participants were originally under the CKD umbrella. You will now see this group addressed in all our filters along with CKD, AKI, and Healthy Reference tissue types.
  • File name identifier - The long identifier prefix on file names has been removed for better readability. It is still viewable if you select File UUID from the table column chooser.
  • Improved scrolling - Table and filter panel scrolling behavior has been improved for both Spatial Viewer and Repository
  • Recently Released - In the Repository you can now click on the “Recently Released” check box on the File tab to select only those files that are new or updated in the current release.
  • ‍Participant Portal - Spanish language translation available

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MARCH 2023 (v9.0)

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ATLAS REPOSITORY

New data available

See: Atlas Data Release Notes

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ATLAS SPATIAL VIEWER

New spatial data available:

  • Light Microscopy Whole Slide Images (196)
  • Spatial Lipidomics (86)
  • Spatial Metabolomics (25)
  • CODEX (6)

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New feature - Participant Information:

By clicking on the Participant ID, in either the file list or when viewing an image, users will be able to view the Participant Information panel. This panel contains participant-specific information (e.g. disease, age, eGFR) and data available within the Atlas for that specific participant.

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Spatial Metabolomics links updated

The links taking users out to METASPACE have been updated to direct users to a summary landing page for the sample selected. From there, users can navigate to the spatial views with detailed annotations of the data by selecting “Browse annotations”.

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NOVEMBER, 2022 (v7.0)

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ATLAS REPOSITORY

New data available

See: Atlas Data Release Notes

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SEPTEMBER, 2022 (v6.0)

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ATLAS SPATIAL VIEWER

New image types available

  • Spatial Metabolomics 
  • Spatial N-glycomics 
  • Spatial Lipidomics

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ATLAS REPOSITORY

Changes to Participant ID display

  • When a file contains information for more than one participant, “Multiple participants” will appear in the participant column instead of the list of participants

New data available

See: Atlas Data Release Notes

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JULY, 2022

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Atlas Spatial Viewer

New image types available:

  • CODEX images for 11 participants

New data available:

  • Level added as a data type to be made viewable in the table 
  • 259 additional Whole Slide Images 

Software Applications Help documentation

  • Updated to include documentation on the CODEX images.

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Atlas Explorer

Improved gene search

  • Allows two-letter gene searches.
    Please note that some two-letter genes may not show up in the search as there is a cutoff.
    Users can also search by known aliases that have more than two letters.

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