chimerax-ome-zarr

Plugin providing (limited) OME-Zarr v0.4 support for ChimeraX.

Currently supported:

• zyx-order multiscale volumes.
• Opening local or remote zarr files
• Loading specific multiscales as volumes (streamed on demand and cached in memory)
• Loading all multiscales as a single Volume, accessible using Chimerax's step setting

Currently not supported:

• Labels data
• Channel axes
• Time axes
• non-integer scaling
• translation transformations
• 2D data
• multi-image files

Contributions are welcome.

Installation

From the ChimeraX toolshed

Now available on the ChimeraX toolshed! To download and install run this in the ChimeraX command prompt:

toolshed reload available
toolshed install ome-zarr

From GitHub release

1. Install ChimeraX
2. Download the most recent build from the releases page.
3. Run the following command in the ChimeraX command prompt to install the plugin:

toolshed install /path/to/ChimeraX_OME_Zarr-0.5.3-py3-none-any.whl

4. Restart ChimeraX

Usage

This plugin integrates with the ChimeraX open-command.

To open a local OME-Zarr file:

open /path/to/file.zarr

To open a remote OME-Zarr file:

open ngff:s3://bucket-name/path/to/file.zarr

To open a remote OME-Zarr file and load specific scales:

open ngff:s3://bucket-name/path/to/file.zarr scales 1,2

NOTE: in order to open files from remote locations other than S3, you may have to install additional python packages (e.g. smbprotocol for SAMBA shares).

Zarr store backend authentication

Authentication to the Zarr storage backend (e.g. S3) may fail if ChimeraX is launched without the appropriate environment variables present.

MacOS

To prevent auth problems, make sure necessary environment variables are set in ~/.zprofile. This plugin will attempt to set these variables automatically if they are not present.

Alternatively, launch ChimeraX from a shell that has the necessary environment variables set. Typically the executable should exist in a location similar to:

/Applications/ChimeraX-1.7.1.app/Contents/bin/ChimeraX