BigDataViewer-based tool for browsing multichannel multiscale N5 datasets.

To install the application as a Fiji/ImageJ plugin, run the following:

mvn -Dimagej.app.directory=<path to Fiji> clean install

Then, it will be available in Fiji under Plugins -> BigDataViewer -> N5 Viewer.

The application expects a path to a directory structured as follows:

/attributes.json

/c0/attributes.json
/c0/s0/
/c0/s1/
/c0/s2/
/c0/...

/c1/attributes.json
/c1/s0/
/c1/s1/
/c1/s2/
/c1/...

...

Root attributes are used as defaults for all channels. They can be overridden by setting channel-specific attributes.

s0, s1, s2 are standard N5 datasets that represent scale levels for each channel. s0 corresponds to full resolution.

Example of the attributes.json file:

{
  "scales":[[1,1,1],[2,2,1],[4,4,2],[8,8,4],[16,16,9],[32,32,17]],
  "pixelResolution":{"unit":"um","dimensions":[0.097,0.097,0.18]},
  "affineTransform":[[1,-0.30,-0.25,0],[0,1.25,0,0],[0,0,0.85,0]]
}

The changes made to the viewer state are saved automatically to bdv-settings.xml file in the root N5 directory:

• brightness & contrast
• color scheme
• display mode (fused/single, interpolation)
• channel grouping
• channel transformations
• bookmarks

To prevent concurrent modification, exclusive file locking is enforced, and the application will warn and suggest to open in read-only mode if somebody is already browsing the dataset.

The application has a built-in cropping tool for extracing parts of the dataset as a ImageJ image (can be converted to commonly supported formats such as TIFF series).

Place the mouse pointer at the desired center position of the extracted image and hit SPACE. The dialog will pop up where you can specify the dimensions of the extracted image.

The image is cropped without respect to the camera orientation in the viewer, so the cropped image will always contain Z-slices.