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FAQ

Q: What types of assays and file types does Rakaia support?​

Rakaia can support the following file types and directory structures:

  • .mcd files for Imaging mass cytometry
  • .txt files containing IMaging Mass Cytometry data
  • .tiff and .ome.tiff for both pyramidal and non-pyramidal tiffs for various image types
  • .h5ad files with spatial coordinates in .obsm['spatial'] for any type of compatible spatial technology such as 10x Visium, Xenium, etc.
  • spatialdata zarr directories containing 10x Genomics assays
  • various file types for Whole slide images (WSI) such as H&E and microscopy:
    • tiff (pyramidal)
    • svs
    • btf (big TIFF)
    • ndpi (Hamamatsu)
    • scn (Leica)
    • jpg/jpeg (lossy compressed)

Q: What are the options for image export in Rakaia?​

A: Rakaia enables image export in full-resolution tiff, HTML, and low-res PNG format. The type of image export required (whether publication-quality or not) will help to inform which format should be used.

The tiff export gives the highest resolution possible for a canvas image, but importantly DOES NOT include the legend or scalebar, as these elements are part of the canvas component and are projected on top of the image. These elements are included in the HTML export, which also has some minimal interactivity such as zooming and panning on the static image. Finally, PNG exports give a low-resolution, static version of the canvas image.

For publication-quality images, it is recommended to either export the HTML form, and then screenshot the image once sized appropriately in the browser, or to simply screenshot the canvas. The screenshots provide quite good resolution for the images and render well in slide presentations and scientific manuscripts.

Q: Can Rakaia support multiple sessions at once?​

A: Yes! Rakaia can support multiple sessions for either a single user or multiple users.

For a single user running rakaia locally on their computer, multiple sessions can be run in parallel by opening up multiple URLs where Rakaia is running (i.e. http://127.0.0.1:5000/rakaia/ can be opened in multiple browser windows simultaneously.) Each session can contain different datasets, and any data changes applied in one session will not affect the other.

For multiple users, Rakaia can be run through Docker and deployed on a shared resource such as a Linux rack server. An example command used by our group to run Rakaia for multiple group members:

docker build -t rakaia .
docker run -p 5000:5000 -v /home/shared/:/home/shared/ rakaia:latest rakaia -da -p 5000 -tr 24

Q: I have set various parameters in my session and I want to save them to come back to a session later. Is this possible?​

A: Yes! in Rakaia various session parameters such as the channel blending parameters set for a panel, various masking settings, etc. can be saced in JSON format (see here for how to export these parameters). The JSON exported can then be re-imported into a new session with the matched imaging data to recreate a past session.

These parameters can also be saved in a custom mongoDB database, which allows users to easily rereate sessions from cloud stores.

Currently, Rakaia does not maintain persistent session, meaning that a page exit or refresh triggers a fresh session without retaining past session data. Enabling persistent sessions part of the current Rakaia roadmap and a feature that we are aiming to add in the near future.