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Getting started

From your first look to sharing your own data.

Open TissUUmaps​

TissUUmaps runs in your browser, with nothing to install.

Open TissUUmaps

Explore an example​

Open a project from the gallery. Pan and zoom in the viewer, and show, hide or restyle each image, label, point and shape layer in the side panel.

Gallery

Add your own data​

Local data

Chrome, Edge and other Chromium-based browsers only. Not available in Firefox or Safari.

Drag the folder with your data onto the Project tab to connect it, then click Start empty. Now drag files or folders, such as an OME-Zarr store, from that folder onto the Images, Labels, Points, Shapes or Tables tab. TissUUmaps recognizes the format and fills in the add dialog.

Cloud data

All browsers.

Click Start empty, then Add image (or labels, points, shapes, table) in the matching tab and paste the URL of your data. The server must allow cross-origin requests (CORS).

See the supported data for the formats and their settings.

Open a SpatialData store​

info

The SpatialData plugin is still in development. It will become part of TissUUmaps itself in a future release.

The SpatialData plugin reads a whole SpatialData store. Open the plugins menu (⋮ in the tab bar), choose Load plugin from URL… and paste:

https://tissuumaps4.serve.scilifelab.se/plugins/spatialdata.js

In the new SpatialData tab, paste the URL of a store and click Load. For a store on your computer, first connect the folder that contains it (see Local data above), then click Choose a store in the connected folder and pick the .zarr folder.

The tab lists the images, labels, points and shapes of the store by coordinate system. Add the ones you want and color them by the store's tables.

Save and share​

Download project in the project menu saves a project file (.tm4). It describes your data and how to show it, but does not contain the data. Drop it on the Project tab to open it again.

To share a project, put the project file and the data on a web server, and add the project file's URL to the TissUUmaps link:

https://tissuumaps.github.io/app/?project=https://example.org/project.tm4

Paths in the project file can be relative to it, so the project folder can move without editing the file. See Projects.

Learn more​

  • Concepts: projects, data types and coordinate systems.
  • Supported data: the file formats TissUUmaps reads, and how to configure them.
  • Questions and bugs: ask a question or report a problem on GitHub.
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