vscode-wsi-viewer

View whole slide images (WSI) in VSCode. Extension page

Features

• From right click menu, open a WSI file in a new tab.
• Supported extensions are the ones in openslide
  • "svs", "tif", "vms", "vmu", "ndpi", "scn", "mrxs", "tiff", "svslide", "bif"

Requirements

This extension needs wsiserver for patcing and serving WSI files.

• Install python>=3.6 and wsiserver.
  • apt install openslide-tools
  • pip install wsiserver

If you want to open a WSI in a remote host, you need to

• install wsiserver in the remote host.
• set port forwarding to the host. wsiserver runs on port 31791 by default. If 31791 is occupied by other process, wsi-viewer will try to use 31792, 31793, 31794, 31795.
  • e.g. If you are opening the WSI in "remoteHostA" which is in your local network and has 192.168.50.10, in ssh config file,

    Host remoteHostA
        HostName 192.168.50.10
        User tand826
        LocalForward 31791 localhost:31791
        LocalForward 31792 localhost:31792
        LocalForward 31793 localhost:31793
        LocalForward 31794 localhost:31794
        LocalForward 31795 localhost:31795
    

Extension Settings

• Available settings
  • wsiviewer.ports (default: 31791,31792,31793,31794,31795)
  • [TO BE ADDED] wsiviewer.url_template (default: "/{url}:{port}/{z}/{x}/{y}.{format}")

Known Issues

• not yet

Release Notes

1.0.0

Initial release of vscode-wsi-viewer.

1.1.0

Enabled for remote servers.

1.1.1

Error message updated for wsiserver path.

1.1.3

README updated with new sample images.

1.1.4

User can open multiple wsis at a time with portforwarding settings.

1.1.5

Code visibility changed to public with some new instructions in README.

1.1.7

README updated with an animated gif.

1.1.9

Security update.