CytoCanvas is where your data comes alive. Overlay segmentation masks on high-resolution images to confirm that cells were identified correctly, then toggle between modalities to see RNA transcripts, proteins, and organelle markers within clearly defined cell boundaries.

From there, you can compare protein intensities, sort and filter cells by morphological traits or target intensities, see which cells are expressing which guide RNA, and isolate phenotypes for side-by-side comparison. You can also customize images for publication and share specific views and cell groupings with your collaborators.

Cytos data is available in standard formats, so it works with open-source tertiary tools and lets you extend your tertiary analysis. Each run produces a Spatial Data Object (SDO), a standard format supported by the scverse ecosystem. Combining multimodal readouts into a single data structure, the AnnData table includes a row for each cell with aligned 3′ counts, more than 100 CellProfiler metrics for each morphology and protein target, guide RNA counts, and associated metadata.