> For the complete documentation index, see [llms.txt](https://www.parapathology.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://www.parapathology.com/computational-digital-and-mathematical-pathology/digital-pathology-software/celldega.md).

# Celldega

A source-available visualization toolkit and spatial biology exploration engine developed by the Broad Institute of MIT and Harvard (Fernandez, Ishar, Wang, Ben Saad, Lipinski & Farhi, *bioRxiv* 2026). Celldega is engineered to address the scalability bottleneck of client-side spatial omics and multiplexed digital pathology datasets (>1 billion transcripts, millions of segmented cells) by leveraging browser-native streaming, GPU-accelerated rendering, and specialized columnar storage formats.

* **Documentation & Web Viewer:** [broadinstitute.github.io/celldega](https://broadinstitute.github.io/celldega/)
* **GitHub Repository:** [broadinstitute/celldega](https://github.com/broadinstitute/celldega)
* **Preprint:** Fernandez et al. *Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data.* bioRxiv (2026). [DOI: 10.64898/2026.08.13.744672v2](https://doi.org/10.64898/2026.08.13.744672v2)
* **Interactive Notebook Demo:** [marimo interactive notebook on molab](https://molab.marimo.io/notebooks/nb_A6JG5XUg5EPJyMwNDcsM18)

**License checked 1 October 2026:** The upstream [LICENSE.txt at commit `726b57c`](https://github.com/broadinstitute/celldega/blob/726b57cfeff1a0e70b06b91b079bd592b91daeca/LICENSE.txt) is the Broad Institute Academic Software License. It grants specified educational and academic-research uses to academic/nonprofit researchers and directs commercial entities to Broad for licensing. Read the full terms before use or redistribution. This check concerns the license only; the research and performance summary below was not re-evaluated.

***

## Architectural Highlights & Innovations

### 1. DegaFiles and Row Group Spatial Indexing

Traditional spatial transcriptomics data storage splits multiplexed datasets into tens of thousands of fragmented files or bulky monolithic tables that overload browser memory. Celldega introduces **DegaFiles**, an open storage convention built on Apache Parquet and GeoParquet:

* Consolidates 50,000+ individual coordinate/feature files into \~10 structured Parquet tables.
* Employs spatial indexing where spatial tile coordinates map directly to Parquet row groups (`row_group_index = tile_x * num_tiles_y + tile_y`).
* Utilizes byte-range HTTP streaming via WebAssembly (`parquet-wasm` and Apache Arrow), fetching only the precise byte chunks needed for the user's active viewport without requiring server-side Python kernels.

### 2. GPU-Accelerated Multi-Layer Rendering

Built on [deck.gl](https://deck.gl/) and HTML5 Canvas, Celldega renders hundreds of millions of spatial data points, polygonal cell segmentations, and multi-channel image pyramids concurrently at 60 fps:

* **Spatial Alignment:** Co-registers high-resolution whole-slide brightfield/fluorescent imagery with single-cell transcriptomic annotations.
* **Dynamic Shading & Gating:** Real-time client-side expression thresholds and cluster re-coloring without server re-computation.

### 3. Specialized Analytical Views

Celldega provides distinct visualization modalities:

* **Landscape View:** 2D multi-layer spatial exploration of tissue sections, combining cell segmentation masks and individual transcript dots.
* **Yearbook View:** High-throughput single-cell gallery displaying isolated morphology across phenotypic clusters.
* **CellCloud & NeighborhoodCloud:** 3D orbital embedding visualizers linking dimensionality-reduced manifolds (UMAP/t-SNE) directly back to spatial coordinates.
* **Clustergram & Composition:** Interactive heatmaps displaying cell type compositions across histological tissue zones.
* **Enrich:** Direct integration with Enrichr for immediate pathway and gene-set enrichment queries from selected spatial regions.

***

## Comparison with Existing Spatial Systems

| Dimension               | Cytario                                             | Celldega                                                 | Vitessce                                     |
| ----------------------- | --------------------------------------------------- | -------------------------------------------------------- | -------------------------------------------- |
| **Primary Scope**       | Image Management System (IMS) & clinical WSI viewer | Spatial omics & multiplexed transcriptomics analytics    | General bioimaging & spatial omics dashboard |
| **Backend Storage**     | S3 object store (OME-Zarr, OME-TIFF, GeoTIFF)       | DegaFiles (GeoParquet / Parquet with row-group indexing) | Zarr / AnnData / OME-TIFF                    |
| **Streaming Mechanism** | DuckDB-WASM & Viv multi-scale tiles                 | Parquet-WASM byte-range streaming via deck.gl            | Viv multi-resolution loaders                 |
| **Target Workload**     | Petabyte-scale clinical digital pathology workflows | Billion-transcript spatial exploratory analysis          | Multimodal exploratory dashboards            |