Web-based viewers
Vizarr (2D + Channels)
Create a link by pasting the address of the dataset after the =
in the following link:
For example, paste the following address:
Thus construct the following link:
https://hms-dbmi.github.io/vizarr/?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BSST410/IM2/IM2.zarr/0
Click on it or paste it in the browser to open the viewer.
itk-vtk-viewer (3D + channels)
Create a link by pasting the address of the dataset after the =
For example, paste the following address:
Thus construct the following link:
https://kitware.github.io/itk-vtk-viewer/app/?fileToLoad=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BSST410/IM2/IM2.zarr/0
Click on it or paste it in the browser to open the viewer.
Allen 3D Volume Viewer (4D + channels)
Create a link by pasting the address of the dataset after the =
For example, paste the following address:
Thus create the following link:
https://volumeviewer.allencell.org/viewer?url=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BSST410/IM2/IM2.zarr/0
Click on it or paste it in the browser to open the viewer.
Neuroglancer (2D + channels, volume rendering experimental)
- Go to https://neuroglancer-demo.appspot.com/
- On to top right in
Source, paste the following: - Press Enter (multiple times).
- Navigate around in the sample
- Zoom in/out:
ctrl + mouse scroll - Neuroglancer enables sharing of views. The URL in your browser adapts to your current view. Simply copy and paste the URL to share a view with a collaborator
BioImage Archive
The BioImage Archive also provides visualisations for the datasets they store, using the tools discussed above.
Click on the link below to see an example.
https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BSST410/IM2.html
An advantage of the BioImage Archive is that they also provide a range of image metadata along with the visualisation.