The Workspace
Relay’s workspace is a desktop. It has windows you move and resize, a menu bar across the top, and one dock along the bottom that holds your apps, the Ray assistant, and the tools for whatever you are looking at. Everything runs in your browser.
The five apps
Section titled “The five apps”The dock holds one icon per app. Clicking an icon opens it; clicking it again brings its window back to the front. Under each icon is one dot per open window: solid green while the window is on the desktop, a yellow ring once you have minimized it. When an app has several windows, clicking its icon lists them by name so you can pick the one you want, minimized ones included.
Data
Every file you can reach, in one tree — this computer, your Relay Drive, and anything you connect.
Commons
Public datasets from DANDI, IDR and the Allen Institute, ready to open without downloading.
Notebooks
Real Jupyter notebooks in Python or R, with an optional cloud GPU behind them.
Conductor
Workflows you can run over a whole folder, schedules that run them for you, and every run they produced.
Studio
Turn results into slide decks, papers and posters.
There is one more window that you never open cold: Viewer. Opening a file gives it its own Viewer window, so a new file never replaces what you were already looking at. While any Viewer window is open, a Viewer icon joins the end of the apps in the dock, listing your open files so a minimized one is easy to bring back.
Moving and hiding the dock
Section titled “Moving and hiding the dock”The dock slides out of the way a couple of seconds after your pointer leaves it, and comes back when you move the pointer to its edge of the screen. It stays put while you have a conversation with Ray open or while Ray is working. To keep it on screen all the time, right-click the dock and choose Keep dock visible. Beside a maximized window it still steps aside, since the window runs edge to edge.
Drag the dock by any empty part of it to move it to another edge: a soft glow shows where it will land, and lights up once you are close enough to drop. Letting go anywhere else puts it back. On the left or right edge the dock turns vertical, Ray rests as its icon, and a conversation opens beside the dock rather than above it. The same choices are in the right-click menu under Position, and in the command palette (⌘K) as Dock: Move to…. Arranging or fitting your windows keeps them clear of the dock wherever it is.
The dock never grows past the edge of the screen. When space runs short, for example with a conversation open on a small laptop, the apps fold into a single Apps icon that opens the full list, and they unfold again as soon as there is room.
The tree
Section titled “The tree”Local Disk is this computer. Relay Drive is your cloud storage. Anything you connect appears underneath as another root — same tree, same right-click menu, wherever the bytes actually live.
Drag files onto the Data window, or straight onto its dock icon, and they land in Local Disk. Large files upload to your Drive in the background while you keep working.
Connecting a source
Section titled “Connecting a source”The + button in the Data window’s toolbar opens the integrations picker. Connect a source once and its files appear in the tree — nothing is copied until you open it.
| Category | Sources |
|---|---|
| Cloud storage | Google Drive, Dropbox, OneDrive, SharePoint, Box, Amazon S3, Google Cloud Storage, Azure Blob, Backblaze B2, Wasabi |
| Research | OSF, Zenodo, Figshare, Dryad, Globus, Hugging Face |
| Genomics | NCBI, AWS Open Data |
| Imaging | OMERO |
| Neuroscience | DANDI, OpenNeuro |
You can also paste a direct URL to a file or a Zarr store.
Folders that make themselves
Section titled “Folders that make themselves”Two folders in your Relay Drive fill themselves in as you work:
Notebooks/— every notebook you create is saved here automatically, with version history.Studio/— decks, papers and posters you build in Studio.
They are ordinary folders. Open, rename, share, download or delete what’s in them from the Data app like anything else — which means the notebook you wrote yesterday is findable in the same place as the data it read.
Previewing and opening
Section titled “Previewing and opening”Selecting a file previews it: real dimensions, channels and size, read from the file rather than guessed from its extension. Opening it (double-click, or the preview’s Open button) routes it to the right app — notebooks to Notebooks, Studio documents to Studio, everything else to a Viewer window of its own.
Notebooks
Section titled “Notebooks”Write and run cells
Standard
.ipynb— cells of Python and Markdown, run one at a time or all at once. Anything you write here opens in Jupyter or VS Code, and anything you already have imports without conversion.Pick a runtime
The Runtime control is the whole cloud-compute story. Stay on CPU, or switch to a T4, A10G or A100 and the notebook reconnects to that machine.
It lives in the notebook’s Inspector — open it from the tool cluster at the bottom of the screen, or pop it out into its own window. The Inspector is empty until a notebook is actually open, along with the kernel controls, version history and fork.
Nothing to install or provision, and you are billed only while it runs — so take the big GPU for the training cell and drop back to CPU afterwards. Switching restarts the kernel, so do it before you build up state you care about.
Reference a file instead of typing a path
Insert file reference, from a cell’s ⋮ menu, lists everything in the Data app and drops in the code that opens what you pick. It works the same whether the file is on your disk, in your Drive, or on a source you connected — you don’t have to know where it lives.
Let it save itself
Notebooks save to
Notebooks/in your Drive as you work, with version history you can roll back from the notebook’s own menu.
Processing
Section titled “Processing”Tools live next to the file they apply to. With a Viewer in front, open Controls from the tool cluster at the bottom of the screen and choose the Process tab.
It holds ordinary image processing — a blur, a threshold, a watershed, an FFT — grouped into categories such as Filters, Edge Detection, Morphology and Colocalization.
They run in your browser, the moment you click: no job, no queue, no compute cost. Each one stacks on the image as a layer you can toggle, reorder or delete, and your file on disk never changes. If you’ve selected a region, the tool applies to just that region. See Processing tools.
Any tool can become a step in a workflow, which Conductor can then run over a whole folder or on a schedule.
Conductor
Section titled “Conductor”Three sections: Workflows, Schedule and Runs. Build a chain of steps once, run it over a folder, set it to run on a clock or whenever a file arrives, and see every run and why a step failed. See Conductor and Automation.
Studio
Section titled “Studio”Slide decks, papers and posters, built from data you already have open rather
than from screenshots pasted into another app. Decks play full-screen with real
transitions, and everything you make is saved to Studio/ in your Drive.
When a deck is open, a ▶ Present button appears in the tool cluster at the bottom of the screen.
Manuscripts
Section titled “Manuscripts”Open a paper from the Data app to work on it in Studio. The manuscript editor keeps the section outline, source, figures, citations and compiled PDF together with the data used to make them.
- Write gives you section-focused editing while preserving LaTeX commands, figure references and citations.
- LaTeX gives you the complete source when you need to edit arbitrary LaTeX.
- Figures lets you review available figure revisions and apply an update to the manuscript.
- Commons lets you add a source citation with its evidence attached.
- Ray’s mark in the toolbar tags the paper in the chat bar, so Ray works from the manuscript and its linked data.
- PDF compiles the current manuscript, while history keeps earlier source and figure revisions available.
Manuscript editing is collaborative. Share the manuscript with collaborators and their changes appear live as they work. The same permissions control who can view or edit it.
Studio can compile a manuscript and package its source and figures as a publication release. Publishing remains an explicit step; editing a draft does not automatically publish it. Canvas remains a separate workspace for data exploration and draft composition.
The menu bar
Section titled “The menu bar”Account
Profile, password and two-factor, plus the API tokens that let your own scripts, editors and agents reach your data.
Plan & usage
Your plan, billing, per-run compute usage, how much of your Drive is left, and your Ray activity: every run, what it cost, and a Stop for the ones still going.
Team
Invite people into a shared Space, see who’s in it, and send us feedback.
Appearance
Light, dark or follow your system; the desktop background; and Organize windows for when things get untidy.
Windows
Every open window by name, each with a dot: green on the desktop, yellow when minimized, and a count of the minimized ones on the menu itself. Click a dot to minimize or bring back just that window. Also Fit all windows, Organize windows, Show all and Minimize all. On a narrower Relay window the menu shrinks to an icon.
Help
The command palette, and this documentation in a window. Also where you replay Ray’s tour.
On the right of the bar:
- Share sends a link to the window you have in front — the same file, the same zoom, the same annotations. Recipients don’t need an account, and you can revoke access any time.
- Your avatar is a shortcut into profile, settings, feedback and sign-out.
Sticky notes
Section titled “Sticky notes”Right-click an empty part of the desktop and choose Add note here to leave a note on the wallpaper. Drag a note to move it; it stays where you put it. Each note holds a reply thread and can be resolved or deleted. Notes are saved with the project, so they travel with it when you share it.
Keeping windows under control
Section titled “Keeping windows under control”Minimizing a window (⌘⇧M) takes it off the desktop without closing it. It stays listed in the Windows menu and under its app’s dock icon with a yellow dot. Click the dot to bring it back, or click a green dot to minimize that window: the list stays open, so you can put several away in one go. If a window ever comes back looking wrong, ⌘⇧L (Refresh Window) reloads just that window.
Double-click a window’s title bar, or press ⌘⇧F, to maximize it. A maximized window fills the whole desktop under the menu bar, and the dock, with Ray and the tools in it, tucks out of the way. Move your pointer to the dock’s edge of the screen to bring it back.
⌘⇧↑ brings every minimized window back, ⌘⇧→ and ⌘⇧← step through the open windows, ⌘⇧X closes the one in front, and ⌘⇧Return closes them all. Press G then , to open Settings. Relay avoids ⌘⇧W, ⌘` and ⌘, for these because your browser or your Mac keeps those keys for itself.
When windows pile up, ⌘⇧E fits every window on screen at once, each in its own tile with nothing hidden behind anything else:
- The first press gives the window you are working in most of the desktop and stacks the rest beside it.
- Press again for an even grid.
- Press once more to put every window back exactly where it was.
Windows you had already minimized stay minimized. On a small screen with a lot open, Relay minimizes the windows you have used least recently rather than shrinking everything past the point of being readable, tells you how many, and brings them back on the third press.
Organize windows (⌘⇧A) is the lighter option: it groups windows by app, so several files from one app share a spot and overlap a little. ⌘⇧O flips through your windows like a deck of cards.
The text box in the middle of the dock is Ray. Ask in plain English: open the kidney slide, segment these cells, plot column three. Ray can see whichever window you have in front, so “this file” means the one you’re looking at. When you send a question, that part of the dock grows into the conversation while the apps and tools stay where they are. The box grows a line at a time as you type, so a long question stays in view.
⌘J puts your cursor in the box from anywhere, opening Ray first if it is resting as its icon.
Ray does not have to stay in the dock: drag its bar out of the dock and it becomes a window of its own that you can move and resize. See Ask Ray.
Ray follows the instructions written on the active Project’s home, keeps a record of every run in your Ray activity, and is reachable from Slack, an AI coding tool, or the command line as well as this bar.
The tool cluster
Section titled “The tool cluster”The panel at the end of the dock, after Ray, carries the tools for whatever you’re currently looking at, and changes with it: brightness and channels for an image, playback for video, gating for flow cytometry, a gene picker for single-cell data, the runtime and kernel for a notebook.
It appears only once a window with something in it is in front. On an empty desktop there is no cluster at all — that’s expected, not a bug.
What’s new
Section titled “What’s new”The paper note in the bottom-left corner is a short, plain-language list of what changed recently — no version numbers, no release notes. Close it and it comes back only when something new ships. Windows always paint over it, so it never covers what you’re working on.