Cytogence Atlas Omics
A platform for spatial omics and multi-omics analysis — rolling out in stages. Available now to invited clients: a secure portal to access the figures, reports, and data from your project, each traceable to the analysis that produced it — now with Ask Atlas, an AI assistant that answers questions grounded in your own deliverable. The full self-service analysis suite is coming next.
Access is invite-only during the preview. See what's rolling out ↓
Your deliverables, delivered securely
We run the analysis — you access the results. The Atlas client portal is live in invite-only preview. Log in to browse and download your project's figures, reports, and datasets in one place, with the provenance behind every output a click away. No more zip files, shared drives, or hunting through folders.
Secure, passwordless login
Sign in with an emailed one-time code — nothing to remember, nothing to leak.
Everything in one place
Figures, reports, and data for each project, organized and versioned by delivery.
Provenance on every file
Trace any figure or number back to the analysis, parameters, and inputs behind it.
Comment & collaborate
Ask questions and leave notes right on a deliverable — your analyst is notified.
Already a Cytogence client?
Sign in to the Atlas portal to access your project deliverables.
Client LoginAtlas is in pre-alpha, invite-only access while we expand the preview. Tell us about your project and we'll get you set up with a portal account.
Request AccessAsk Atlas only sees this deliverable. Verify anything you act on.
Ask questions about your results — grounded in your data
Ask Atlas is an AI assistant built into every deliverable. Ask what a finding means, how groups compare, or where a number came from — and get a clear answer grounded only in that deliverable's report, tables, figures, and provenance. No web searches, no other projects, no guesswork.
Grounded in your deliverable
Answers come only from your report, data tables, figures, and provenance — never the open web or other projects.
Citations to the source
Every answer links back to the exact report section or figure, so you can verify it in one click.
Key Takeaways & Expert mode
Open with an instant summary and suggested questions, or switch on Expert mode for deeper reasoning on tougher questions.
Private & opt-in
Off until you turn it on. Your data is never used to train AI models, and the AI provider retains nothing once it answers.
GeoMx-Native
Plug-and-play DCC/PKC import. No preprocessing scripts.
Full Provenance
Every output traceable to its data, parameters, and code version.
Publication-Ready
Static and interactive figures. Export as SVG, PDF, or PNG.
No Coding Required
Full GUI. Download, install, analyze. No R or Python setup.
End-to-end spatial and multi-omics analysis
Atlas is growing into a full analysis platform — from raw data import through publication-ready figures and client deliverables, in one workflow. Here's what we're building, available to clients as the preview expands. Today these analyses run in-house; we deliver the results to your portal.
Smart data ingestion
Atlas automatically detects data layout, transposes matrices when needed, merges metadata, and identifies column types. Just drop your files in.
GeoMx DSP Native Import
Direct DCC + PKC file import. Parses probe kits, builds expression matrices, extracts QC metrics — no preprocessing scripts needed.
Universal Expression Matrices
CSV, TSV, and TXT with smart detection. Auto-identifies genes-as-rows vs. samples-as-rows and transposes when needed.
File Integrity Tracking
SHA256 hashing, file size, row/column counts, and format detection for every imported dataset.
Research-grade analysis modules
A growing library of analysis modules powered by Python's scientific stack — NumPy, SciPy, scikit-learn, scanpy, and gseapy — accessible through a clean graphical interface.
Differential Expression
Parametric (t-test) and non-parametric (Mann-Whitney U) testing with Benjamini-Hochberg FDR correction. Automatic volcano plots.
Cross-Compartment Analysis
Correlate features across spatial compartments — tumor vs. stroma, epithelial vs. immune — with Manhattan-style visualization.
Pathway Enrichment
EnrichR ORA and pre-ranked GSEA across KEGG, Reactome, GO, MSigDB Hallmark, and WikiPathways — with dot plot visualization.
Correlation & Stratification
Pearson and Spearman correlation with full matrix, target-specific, and group-stratified modes. Clustered heatmaps included.
Dual-Render Figures
Every analysis generates both static (matplotlib, publication-ready) and interactive (Plotly, zoomable/hoverable) figures simultaneously.
Report Builder
Drag-and-drop blocks — text, figures, tables, headings — into curated reports. Export as self-contained HTML, print to PDF.
Data Inventory Browser
Tree view of every dataset, analysis run, and output. Click any result to trace it back to its source data, parameters, and code version.
Composable Pipelines
Use outputs from one analysis as inputs to the next. Build analysis chains — differential expression to pathway enrichment to report — with full traceability.
Desktop + Server
Run as a native desktop app (Windows, macOS, Linux) or deploy as a headless server for shared lab access via any browser.
Bundled Environment
Python scientific stack included. No R, Python, or conda installation required. Download, install, analyze.
Built for spatial omics workflows
Atlas was designed around the real-world workflows of spatial omics research — from GeoMx DSP data import through cross-compartment analysis and client-ready deliverables. Future releases will expand support to 10x Visium, CosMx SMI, Xenium, and single-cell platforms.
How Atlas fits in your workflow
Atlas fills the gap between raw spatial data and publishable results — the step where most teams spend weeks writing custom scripts.
Custom R/Python scripts. Manual file tracking. Copy-paste into PowerPoint. Results not reproducible by collaborators.
Import data, run analyses, generate figures, build reports. Every output traceable. Share projects with collaborators.
Publication-ready figures. Client-ready reports. Full provenance. Reproducible analyses. Weeks saved per project.
Interested in Atlas Omics?
The client portal is live in invite-only preview, with the full analysis platform rolling out next. Already a client? Sign in below. Otherwise, get in touch and we'll get you set up.