AtlasXomics Documentation

Welcome to the documentation for the AtlasXomics (ATX) spatial-omics data processing platform. AtlasXomics has developed a suite of tools that enable scientists to process spatial-omics data both on the cloud and locally. Here we provide comprehensive, end-to-end documentation for that platform.

Platform overview

Raw data consists of FASTQ and image files. From these, ATX supports two primary processing paths and an optional combined path:

• Epigenomics — spatial ATAC-seq and CUT&Tag
• Whole Transcriptome — spatial RNA-seq
• Co-Profiling — an optional path that combines epigenomic and transcriptomic secondary outputs

Our standard processing pipeline runs on the LatchBio cloud platform. Outputs are stored in the Latch File system (Latch Data) and visualized in Plots. Image data can be processed with AtlasXBrowser on a Latch Pod or locally. We also provide guidance for "DIY" processing on a local machine.

Data flow at a glance

    FASTQ                                images
      │                                    │
      ▼                                    ▼
 Preprocessing / QC                   AtlasXBrowser
      │                                    │
      ▼                                    ▼
 Optimization (parameter sweeps) ◄──── spatial folder
      │
      ▼
 Secondary analysis (ArchRProject, AnnData, Seurat)
      │
      ├──────────────► Plots (visualization)
      │
      ▼
 Co-Profiling (optional)   (epigenome × transcriptome)

Every modality (Epigenomics, Whole Transcriptome, Co-Profiling) follows the same overall shape. We use consistent stage names throughout this documentation:

1. Preprocessing / QC — alignment and QC of FASTQ files, and processing of image data.
2. Optimization — parameter sweeps that evaluate multiple dimensionality-reduction / clustering settings in parallel to inform final processing.
3. Secondary analysis — post-alignment processing that moves aligned data toward more meaningful context: gene accessibility, peak calling, and motif deviations (epigenomic), clustering, cell typing, and spatial analysis, plus generation of objects (ArchRProject, AnnData, Seurat) for downstream work.
4. Plots — interactive visualization of the results.

Tutorials

Step-by-step, click-through tutorials for running ATX Workflows and tools on Latch are maintained in Scribe.

• AtlasXomics / LatchBio Tutorials (collection)
• Running AtlasXBrowser
• DIY processing of Epigenomic data

Where to start

• Epigenomics Preprocess, optimize, and analyze spatial ATAC-seq / CUT&Tag data.

• Whole Transcriptome QC and secondary analysis for spatial RNA-seq data.

• Co-Profiling Integrate epigenomic and transcriptomic outputs.

• Glossary Latch platform concepts and ATX-specific terms, defined.

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Maintained by AtlasXomics, Inc.