Software Release Notes

2025 December 11: ICM v1.0.1

Fixed Issues

• Fixed an issue where analyses hang in "Pending" status indefinitely.

• Updated the ATAC/ChIP-seq analysis data import node to its correct label.

• Added greater transparency around regional data routing for Correlation Engine pathway analysis.

🎉 2025 December 4: ICM v1.0 (Full Commercial Release) 🎉

New Features & Enhancements

• Expanded Assay and Analysis Support

  • Introduced multiomic analysis capabilities, enabling joint analysis of sample combinations such as proteomics + mRNA and DNA + methylation

  • Enhanced genomic variant interpretation capabilities via filtering variants using public and Illumina databases, including PromoterAI and PrimateAI

  • Added support for additional Illumina and commercial assays, including miRNA, ChIP/ATAC-Seq, DNA-Seq, and NanoString CosMx.

  • Introduced default analysis workflows for 5-base DNA, RNA-seq, and miRNA for streamlined analysis setup.

• Visualization Improvements

  • Introduced visualizations for DNA, including a Chromosome View

  • Enhanced legends for complex plots such as Leiden clusters.

  • Added UMAP animation and export options for spatial plots.

  • Included attribution on exported images for presentations.

  • Improved filtering behavior and performance for large datasets.

• Sample & Metadata Management

  • Introduced a global samples grid for unified sample browsing across studies.

  • Enabled multi-study sample sharing without re-ingestion.

  • Improved metadata syncing between Study Management and Analysis.

  • Added support for resolving duplicate sample name issues.

• Data Import & Study Management

  • Allow for uploading local files to ICA project storage via the ICM UI

  • Streamlined file ingestion workflows, including adding multi-file/multi-folder selection.

  • Enabled on-the-fly ICA project creation during ICM study setup.

  • Improved options for opting in/out of auto-analysis creation for studies.

• Usability & UI Enhancements

  • Refreshed visuals across grids and dialogs.

  • Improved error messaging and log visibility for failed tasks.

  • Enhanced “Send logs” workflow with better user information and messaging.

Bug Fixes

• Analysis & Visualization

  • Resolved intermittent errors and crashes in key workflows including PCA, UMAP, DESeq2, Monocle 3, and Scanpy ScType.

  • Improved task stability for differential expression, motif detection, and trajectory analysis.

  • Resolved issues where analyses appeared complete prematurely or failed to start due to backend errors.

  • Improved handling of large datasets.

  • Fixed issues with plot interactions, floating menus, and missing buttons in the Data Viewer.

  • Improved behavior of transpose and reorder functions in spatial samples.

• Sample & Metadata Management

  • Enhanced feedback for missing files and metadata upload errors.

  • Corrected sample group naming and filtering inconsistencies.

• Authentication & Session Handling

  • Addressed issues with login sessions, token renewals, and stale cookies that caused unexpected logouts or errors.

• UI & Navigation

  • Refined layout and responsiveness in study management, data import wizard steps, and action buttons.

  • Fixed misleading or missing UI elements for better clarity.

2025 September 23: ICM v0.6.1

Enhancements

• Multi-Tab Session Support

  • Multiple studies or analyses can be open in separate browser tabs within the same session and within the same workgroup

• Improved Clustering Defaults

  • The default method for graph-based clustering has been updated to Louvain, offering better performance across data types. Users can still manually select Leiden if preferred

• Minor user interface improvements made to the welcome screen, study tiles, application switcher, data viewer, and error messages

Bug Fixes

• Data Import & Analysis

  • Resolved several issues related to intermittent failures for auto-ingestion, manual import, and analysis creation

2025 August 1: ICM v0.6

New Features and Enhancements

• Expanded Assay Support

  • Illumina Protein Prep: Enhanced metadata handling and new demo datasets.

  • Illumina Spatial Transcriptomics: Added cell-cell interaction analysis.

  • Illumina Spatial Transcriptomics & Illumina Single-Cell 3' RNA: Support for user-defined marker gene files for cell typing.

  • Illumina 5-Base DNA Prep & 5-Base DNA Prep with Enrichment (DNA Methylation):

    • Custom Workflow (User-defined parameters): Methylation QC, Sample Filtering, DMR (DSS), PCA/UMAP, Clustering, Get Regional Methylation, Annotate Regions, Gene set enrichment/Pathway analysis

  • Illumina Infinium Methylation: Custom workflow

  • Third-Party Assays: Introduced broader support for some commercial assays, including:

    • Proteomics

      • Somalogic

    • Spatial Transcriptomics

      • 10x Genomics Visium Space Ranger

      • 10x Genomics Xenium

    • Single-Cell Transcriptomics

      • 10x Genomics Cell Ranger

      • Seurat

      • Sparse matrix for 10x Genomics, Fluent Biosciences, Parse Biosciences

      • AnnData h5ad processed by Scanpy

    • scATAC-Seq

      • 10x Genomics Cell Ranger

      • Seurat

    • Bulk Transcriptomics

      • Gene counts in salmon format

• Usability Enhancements

  • Refreshed UI/UX for data visualization and overall user flow.

  • New tutorial study with demo data and pre-baked analyses for improved onboarding.

  • WalkMe integration for in-app help and guided workflows.

  • Improved error messaging and notifications.

Bug Fixes

• Data Handling

  • Resolved issues with large file uploads, ADAT file metadata, and .h5ad imports.

  • Improved error messages and ingestion reliability.

• UI & Navigation

  • Fixed navigation inconsistencies, missing file labels, and refresh issues.

• Analysis & Tasks

  • Addressed intermittent failures in some analysis tasks.

  • Improved CPU prediction and task runtime tracking.

• Stability & Security

  • Fixed intermittent server errors and task requeueing.

Known Issues

• Some UI elements may still behave inconsistently under heavy load.

• Analyses periodically may hang in "in progress" status, requiring users to start a new analysis.

Known Limitations

• Some non-Illumina commercial assay data is not supported in ICM at this time.

• Third-party spatial transcriptomics custom analysis only supports one sample per analysis.

2025 April 16: ICM v0.5.1

New Features & Enhancements

• Updated the type of analysis automatically created for newly imported single-cell and spatial samples.

• Improved caching and updated a configuration for user-assigned subscriptions

Bug Fix

• Addressed an issue with the user flow for signing the end-user license agreement (EULA)

Known Issues

• Intermittent failures with import and analysis tasks.

Known Limitations

• Non-Illumina assay data is not supported in ICM at this time, including proteomics, single-cell, and spatial.

2025 March 31: ICM v0.5

New Features & Enhancements

• Support for Illumina Multiomic Assays

  • Illumina Protein Prep

  • Illumina Single Cell 3’ RNA Prep

  • Illumina Spatial Transcriptomics

  • Illumina DRAGEN RNA (bulk)

• Pre-configured & Custom Analysis Workflows

  • Default Workflows (Pre-configured)

    • Proteomics: Results in PCA and hierarchical clustering heatmap.

    • Single-cell Transcriptomics: Results in PCA and UMAP visualizations.

    • Spatial Transcriptomics: Results in spatial map with transcript overlay; graph-based clusters plotted on a UMAP and pie chart.

    • Default workflows are automatically initiated for individual single-cell or spatial samples added to an ICM study.

  • Custom Workflows (User-defined parameters)

    • Available for all Illumina multiomic assay types.

    • Includes all default analysis options and additional analysis workflows:

      • Differential Expression

      • Pathway Analysis

      • Gene Set Enrichment

• Scalability & Performance Improvements

  • Up to 10x performance improvement in data import and analysis processing.

  • Single-cell RNA analyses can now be performed with multiple samples simultaneously.

  • New samples can be automatically imported into ICM when they are generated as outputs of a DRAGEN secondary analysis pipeline in a linked ICA project.

• UI & UX Enhancements

  • Simplified UI/UX to improve overall usability, reduce complexity, and streamline user flows:

  • Reworked and consolidated UI components for improved consistency and user experience.

  • Improved information architecture for easier navigation.

Bug Fixes & Technical Debt

• Resolved known issues and made improvements related to technical debt.

Known Issues

• Intermittent failures with import and analysis tasks.

Known Limitations

• Non-Illumina assay data is not supported in ICM at this time, including proteomics, single-cell, and spatial.