The Brain Image Library provides following ways to visualize the data remotely, without signing in:
Neuroglancer allows quick visualization of volumetric multi-resolution multi-channel data in a web browser. It also allows sharing a link to a specific view of the data, to be shared with your collaborators exactly as you are viewing it.
The data for Neuroglancer are served via brAinPI, which allows visualizing different multiscale image file formats through the same API.
Currently supported image formats:
Basic usage:
| Feature | How to Use |
|---|---|
| Zoom (using mouse) | <ctrl> <mouse-wheel> |
| Zoom In (using keyboard) | <ctrl> <equals> |
| Zoom Out (using keyboard) | <ctrl> <minus> |
| Scroll through z-planes | <mouse-wheel> |
| Move image | Grab using <left-mouse-button> and drag image |
| Center image where current mouse pointer is | Move mouse cursor over image then <right-mouse-button> |
| Toggle from 4 panel layout to one screen view | Move mouse cursor over image then <spacebar> |
| Rapid move through x, y, or z planes |
Click on the number associated with x, y, or z (found in upper left corner). Then enter either:
|
| Rotate right | <r> |
| Rotate left | <e> |
| Go through z layers (increasing) | <period> |
| Go through z layers (decreasing) | <comma> |
| Snap image that has been rotated to the closest 90-degree rotation axis | <z> |
| Toggle scalebar on/off that is shown on the image | Place cursor over image, press <b> then move mouse cursor |
Napari-bil-data-viewer is a plugin for napari designed specifically for visualizing BIL data. It has a set of widgets for visualizing different types of data: (a) 272 curated fMOST datasets with associated .swc neuron morphologies, (b) thousands of STPT and other image stacks by providing a URL, (c) multiscale .ome.zarr data by providing a URL, (d) neuron tracings in standard .swc format
Installation and usage instructions are available at our github and at napari hub.
A 2-minute video tutorial on how to use the plugin is available on youtube.
The plugin can be installed from napari GUI through Plugins > Install/Uninstall Plugins menu, by typing 'bil' in the plugin search box and clicking the "install" button when the plugin shows up in search results.
To open the plugin in napari, go to Plugins > napari-bil-data-viewer and select the widget you want to open. The dock widget will appear on the right side of the napari window.
To load one of the curated fMOST datasets, open the Load Curated Datasets widget, select one of the datasets in the dropdown menu (the names correspond to dataset names on the BIL file system) and press the Load Dataset button. An image layer with selected dataset will appear. If the dataset has neuron morphology files associated with it, they will appear in the pre-loaded neurons section of the widget. They can be visualized by checking the checkboxes next to the file names. Currently, visualization of neuron morphologies in 2D is impossible due to limitations of napari shapes layer. In the 3D mode the morphologies will be overlaid on top of the whole brain image in the same scale.
To load an image stack, open the Load Image Stack From URL widget, paste a URL to an image stack (list of inks to individual files) and click the Load Dataset button. To get started, you can paste an example URL to the URL input field by clicking the corresponding link and load the example image stack. Currently supported formats are .tif, .tiff and .jp2 - most common formats for STPT stacks.
To load a multiscale dataset (.zarr or .ome.zarr), open the Load Multiscale Data From URL widget, insert a URL ending in .zarr to the URL input field and click the Load Dataset button. To get started, you can paste an example URL to the URL input field by clicking the corresponding link and load the example dataset.
To load a neuron morphology not included with the curated datasets (both from BIL or other sources), open the Load Neuron Morphology From URL widget, paste a URL ending in .swc into the URL input field and click the Show SWC button. To get started, paste and example URL by clicking a corresponding link and load an example .swc file.
To adjust scale of any layer open in the viewer, open the Layer Scale Controls widget, select the layer you would like to rescale, paste the desired scale (usually, resolution in microns) in z, y and x, and eventually press the Adjust button.
The development of the napari-BIL-data-viewer was supported by the napari plugin enhancement grant from the Chan Zuckerberg Initiative NPE2-00074