Viewers
Opening a file gives it its own Viewer window. Relay reads the file as it is — no conversion step, no upload first for local files — and picks the viewer from what is inside, not just the extension.
What every Viewer has
Section titled “What every Viewer has”The tool cluster at the bottom of the screen changes with the window in front. For a Viewer it holds:
- the drawing and region tools, where the file type supports them (see Annotations & comments);
- Controls — the Inspector, with tabs specific to the file type plus Process and Info;
- Layers — everything sitting on the file: scenes, processing results, annotations and comments.
Any Controls or Layers popover can be popped out with Open in a window so it stays put while you work.
Right-click a Viewer for Split horizontal, Split vertical, Duplicate pane (a copy with the same camera, channels and adjustments, for comparing two settings side by side), Link camera to pan and zoom two panes together, Solo this pane, and Close pane.
To see recordings from one experiment on a shared clock, select them in Data and choose Open synchronized viewer. See Time synchronization.
Microscopy and images
Section titled “Microscopy and images”Opens: OME-TIFF and TIFF, CZI, ND2, LIF, whole-slide formats (SVS, VSI, NDPI, MRXS, QPTIFF, SCN, BIF, IMS), Zarr and OME-Zarr, PNG, JPEG, GIF, BMP, WebP, SVG.
Large images stream in tiles, so a 40 GB slide opens as fast as a thumbnail. Multi-scene files such as CZI list their scenes in Layers.
Controls: Adjust has Brightness, Contrast, Gamma and Threshold, with invert and background removal; Chans shows every channel with its own colour, visibility and contrast limits; About shows what the file says about itself. Z-stacks and time series get sliders with play controls.
Align to… in the image layer panel registers one image to another — rigid, similarity, affine or B-spline — either automatically or from landmark pairs you place on both. See Image registration.
Opens: MP4, MOV, AVI, WebM, MKV.
Controls: Playback — play, pause, Previous frame and Next frame, a Frame box to jump, Rate, Loop, and an FPS override for recordings with wrong metadata. Annotations are per frame, and a frame can be captured into Studio.
Opens: .dcm, .dicom, .ima; drop a whole series folder and it is
enumerated as a stack.
Controls: Window with presets Soft tissue, Lung, Bone, Brain, Liver and Mediastinum (Brightness and Contrast map to window centre and width); Stack for slice navigation; Plane; Link to step two series together; Measure; Info for the header.
Volumes
Section titled “Volumes”Opens: NIfTI (.nii, .nii.gz), Zarr volumes, and the atlases and
connectomes in Commons.
A 3D viewer with orthogonal slices and a rendered volume. Controls: View, Layers, Advanced, Health.
Electrophysiology
Section titled “Electrophysiology”Opens: NWB, HDF5, SpikeGLX (.bin + .meta, dropped together).
Controls: Time for the window and position, Render, Filter (band-pass and common-reference before display), Chans to pick channels, Probe to see them on the probe geometry, and Sort to browse sorted units. The Spike Annotation tool marks events on the trace.
Calcium imaging
Section titled “Calcium imaging”A Suite2p output folder opens as a cell map over the movie with traces beside it. Controls: Cells (detected, accepted and rejected, with the share accepted) and Traces.
A calcium imaging recording in an NWB file opens as traces, one per cell. In Controls, the Time tab has:
- Signal, which lists every signal in the file (for each imaging plane, its raw fluorescence, dF/F and deconvolved events, when the file has them). Pick one to plot it.
- Open ROI map beside traces, which splits the window to show the imaging plane with its segmented cells drawn on it. Click a cell to jump to its trace.
The Behavior tab lists the continuous signals recorded alongside, such as running speed and pupil. Switch one on and it is drawn as a lane under the traces, on the same time axis.
Single-cell
Section titled “Single-cell”Opens: .h5ad, .loom, .mtx, and Seurat .rds (converted on the
server the first time you open it).
An embedding with cells coloured by cluster, sample or gene. Controls: Embed to switch between the embeddings the file contains (UMAP, t-SNE, PCA and any others); Genes to colour by expression; Display; QC for per-cell metrics; Sets to save the cells you lasso and compare them. The region tool defaults to lasso on this viewer.
Genomics
Section titled “Genomics”Genome browser opens BAM, CRAM, SAM, VCF, BCF, BED, bedGraph, narrowPeak,
broadPeak, GFF, GTF, BigWig and BigBed (gzipped too). Type a gene or
chr:start-end into Locus; pick the Genome; add and reorder
Tracks; save Regions; browse variants under VCF; check QC.
FASTQ files open on their own with Quality, Charts and Summary tabs, and Open in genome viewer once aligned.
Sequences (.gb, .gbk, .fasta, .fa, .dna, .ab1, .sbol) open as
a map with Display toggles for cut sites, features, ORFs and GC content,
plus Enzymes, ORFs, Stats and a Legend.
Flow cytometry
Section titled “Flow cytometry”Opens: .fcs; a FlowJo .wsp can be imported alongside it.
Gate with the Rectangle Gate, Polygon Gate, Ellipsoid Gate and Quadrant Gate tools. Stats shows Count, % parent and % total for each gate. Export gate statistics as CSV or JSON, and the density plot as PNG, from Info → Export.
Molecules
Section titled “Molecules”Opens: PDB, mmCIF, SDF, MOL, MOL2, XYZ, and structures from RCSB PDB and AlphaFold in Commons.
Controls: Load, Style (representation and colouring), Chains, Select, Measure for distances and angles.
Tables and plots
Section titled “Tables and plots”Opens: CSV, TSV, XLSX, XLS, JSON.
A table you can sort and filter, and a plot builder: Data picks columns, Axes and Style shape the chart, Stats summarises, and AI asks Ray to make the plot from a sentence. Tables can be inserted live into Studio.
PDFs and documents
Section titled “PDFs and documents”PDFs open with Pages and an Outline, and take comments like any other viewer. Markdown and JSON open as documents. Notebooks open in the Notebooks app.
Plates
Section titled “Plates”A folder of well images becomes a plate: right-click the folder and choose Arrange as plate (Relay suggests the well count). The Wells window shows the layout, lets you change Arrange as and Well shape, and select rows, columns or wells to act on together.
Spatial transcriptomics
Section titled “Spatial transcriptomics”Xenium bundles open as a spatial map with Genes, Filters, Extent and a Run tab.
Exporting a view
Section titled “Exporting a view”Info → Export on any viewer offers Current view (PNG) and the type-specific exports above. To put a view into a paper or slide deck, use Capture view — see Studio.