How to use the neuroglancer.CoordinateSpace function in neuroglancer

To help you get started, we’ve selected a few neuroglancer examples, based on popular ways it is used in public projects.

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github google / neuroglancer / python / examples / interactive_inference.py View on Github external
def __init__(self):
        viewer = self.viewer = neuroglancer.Viewer()
        viewer.actions.add('inference', self._do_inference)
        self.gt_vol = cloudvolume.CloudVolume(
            'https://storage.googleapis.com/neuroglancer-public-data/flyem_fib-25/ground_truth',
            mip=0,
            bounded=True,
            progress=False,
            provenance={})
        self.dimensions = neuroglancer.CoordinateSpace(
            names=['x', 'y', 'z'],
            units='nm',
            scales=self.gt_vol.resolution,
        )
        self.inf_results = zarr.zeros(
            self.gt_vol.bounds.to_list()[3:], chunks=(64, 64, 64), dtype=np.uint8)
        self.inf_volume = neuroglancer.LocalVolume(
            data=self.inf_results, dimensions=self.dimensions)
        with viewer.config_state.txn() as s:
            s.input_event_bindings.data_view['shift+mousedown0'] = 'inference'

        with viewer.txn() as s:
            s.layers['image'] = neuroglancer.ImageLayer(
                source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
            )
            s.layers['ground_truth'] = neuroglancer.SegmentationLayer(
github google / neuroglancer / python / examples / synaptic_partners.py View on Github external
def __init__(self, synapse_path, top_method='min', num_top_partners=10):
        with open(synapse_path, 'r') as f:
            synapse_data = json.load(f)['data']
        self.synapses_by_id, self.synapse_partner_counts = get_synapses_by_id(synapse_data)
        self.top_method = top_method
        self.num_top_partners = num_top_partners

        dimensions = neuroglancer.CoordinateSpace(
            names=['x', 'y', 'z'],
            units='nm',
            scales=[8, 8, 8],
        )

        viewer = self.viewer = neuroglancer.Viewer()
        viewer.actions.add('select-custom', self._handle_select)
        with viewer.config_state.txn() as s:
            s.input_event_bindings.data_view['dblclick0'] = 'select-custom'
        with viewer.txn() as s:
            s.projection_orientation = [0.63240087, 0.01582051, 0.05692779, 0.77238464]
            s.dimensions = dimensions
            s.position = [3000, 3000, 3000]
            s.layers['image'] = neuroglancer.ImageLayer(
                source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
            )
github google / neuroglancer / python / examples / flood_filling_simulation.py View on Github external
def __init__(self):
        viewer = self.viewer = neuroglancer.Viewer()
        self.gt_vol = cloudvolume.CloudVolume(
            'https://storage.googleapis.com/neuroglancer-public-data/flyem_fib-25/ground_truth',
            mip=0,
            bounded=True,
            progress=False,
            provenance={})
        viewer.actions.add('start-fill', self._start_fill_action)
        viewer.actions.add('stop-fill', self._stop_fill_action)
        self.dimensions = neuroglancer.CoordinateSpace(
            names=['x', 'y', 'z'],
            units='nm',
            scales=[8, 8, 8],
        )
        with viewer.config_state.txn() as s:
            s.input_event_bindings.data_view['shift+mousedown0'] = 'start-fill'
            s.input_event_bindings.data_view['keyt'] = 'stop-fill'

        with viewer.txn() as s:
            s.layers['image'] = neuroglancer.ImageLayer(
                source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
            )
            s.layers['ground_truth'] = neuroglancer.SegmentationLayer(
                source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth',
            )
            s.layers['ground_truth'].visible = False
github google / neuroglancer / python / examples / example_overlay.py View on Github external
ix, iy, iz = np.meshgrid(* [np.linspace(0, 1, n) for n in a.shape[1:]], indexing='ij')
a[0, :, :, :] = np.abs(np.sin(4 * (ix + iy))) * 255
a[1, :, :, :] = np.abs(np.sin(4 * (iy + iz))) * 255
a[2, :, :, :] = np.abs(np.sin(4 * (ix + iz))) * 255

with viewer.txn() as s:
    s.layers['image'] = neuroglancer.ImageLayer(
        source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
    )
    s.layers['ground_truth'] = neuroglancer.SegmentationLayer(
        source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth',
    )
    s.layers['overlay'] = neuroglancer.ImageLayer(
        source=neuroglancer.LocalVolume(
            a,
            dimensions=neuroglancer.CoordinateSpace(
                scales=[1, 8, 8, 8],
                units=['', 'nm', 'nm', 'nm'],
                names=['c^', 'x', 'y', 'z']),
            voxel_offset=[0, 3000, 3000, 3000]),
        shader="""
void main() {
  emitRGB(vec3(toNormalized(getDataValue(0)),
               toNormalized(getDataValue(1)),
               toNormalized(getDataValue(2))));
}
""",
    )
    s.voxel_coordinates = [3000, 3000, 3000]
print(viewer.state)
print(viewer)
webbrowser.open_new(viewer.get_viewer_url())
github google / neuroglancer / python / examples / example.py View on Github external
if args.bind_address:
    neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
    neuroglancer.set_static_content_source(url=args.static_content_url)

a = np.zeros((3, 100, 100, 100), dtype=np.uint8)
ix, iy, iz = np.meshgrid(* [np.linspace(0, 1, n) for n in a.shape[1:]], indexing='ij')
a[0, :, :, :] = np.abs(np.sin(4 * (ix + iy))) * 255
a[1, :, :, :] = np.abs(np.sin(4 * (iy + iz))) * 255
a[2, :, :, :] = np.abs(np.sin(4 * (ix + iz))) * 255

b = np.cast[np.uint32](np.floor(np.sqrt((ix - 0.5)**2 + (iy - 0.5)**2 + (iz - 0.5)**2) * 10))
b = np.pad(b, 1, 'constant')

viewer = neuroglancer.Viewer()
dimensions = neuroglancer.CoordinateSpace(
    names=['x', 'y', 'z'],
    units='nm',
    scales=[10, 10, 10])
with viewer.txn() as s:
    s.dimensions = dimensions
    s.layers.append(
        name='a',
        layer=neuroglancer.LocalVolume(
            data=a,
            dimensions=neuroglancer.CoordinateSpace(
                names=['c^', 'x', 'y', 'z'],
                units=['', 'nm','nm','nm'],
                scales=[1, 10, 10, 10]),
            voxel_offset=(0, 20, 30, 15),
        ),
        shader="""
github google / neuroglancer / python / examples / example_skeletons.py View on Github external
data_type=np.float32,
            num_components=1,
        )

    def get_skeleton(self, i):
        pos = np.unravel_index(i, shape, order='C')
        vertex_positions = [pos, pos + np.random.randn(3) * 30]
        edges = [0, 1]
        return neuroglancer.skeleton.Skeleton(
            vertex_positions=vertex_positions,
            edges=edges,
            vertex_attributes=dict(affinity=np.random.rand(2), affinity2=np.random.rand(2)))


viewer = neuroglancer.Viewer()
dimensions = neuroglancer.CoordinateSpace(
    names=['x', 'y', 'z'],
    units='nm',
    scales=[10, 10, 10],
)
with viewer.txn() as s:
    s.layers.append(
        name='a',
        layer=neuroglancer.SegmentationLayer(
            source=[
                neuroglancer.LocalVolume(
                    data=segmentation,
                    dimensions=dimensions,
                ),
                SkeletonSource(dimensions),
            ],
            skeleton_shader='void main() { emitRGB(colormapJet(affinity)); }',