# Software Release Notes ## 2026 March 5: ICM v1.1.1 ### Fixed Issues * Addressed issues regarding analysis task completion stability, plots and figures inconsistently loading, caching inconsistencies, and sharing analyses across studies and workgroups. ## 2026 February 19: ICM v1.1 ### **New Features & Enhancements** * Expanded Assay & Analysis Support * Introduced AI-assisted task recommendations to simplify building multi-step analysis workflows * Added support for additional Illumina and commercial assays, including: * Bulk * Alamar proteomics * Generic count matrices (RNA, miRNA, and protein) * Single cell * Illumina DRAGEN Single Cell Perturb-seq * Count matrices such as BD Rhapsody * Flow/mass cytometry * V(D)J and V(D)J + scRNA-seq * Microarray * Intensity matrix * Illumina Spatial Transcriptomics analysis can be performed on multiple samples * Added ability to export and import analysis workflows to facilitate collaboration and sharing across users and environments. * Visualization Improvements * Added Manhattan Plots for DMR results, enabling clear genome‑wide significance review. * Improved Task Graph and Data Viewer experience, including searchable task menu, updated color palettes, improved legend behavior, and smoother selection interactions. * Data Import & Study Management * Support for folder‑based local file uploads for easier bulk import. * Usability & UI Refinements * Included updated labels, cleaner grids, improved empty states, and auto‑refreshed analysis tiles statuses, better visibility into task errors, and more consistent terminology. ### Fixed Issues * Numerous fixes improving overall reliability, particularly in differential methylation workflows, spatial tasks, metadata handling, plotting behavior, and upload/permission logic. ## 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. ## :tada: 2025 December 4: ICM v1.0 (Full Commercial Release) :tada: ### 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. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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