Utility

Data Helper Methods

class brainlit.utils.NeuroglancerSession(url: str, mip: int = 0, url_segments: Optional[str] = None, fill_missing: bool = True, use_https: bool = False)[source]

Utility class which pulls and pushes data.

Parameters

  • url -- Precompued path either to a file URI or url URI. Defaults to mouselight brain1.

  • mip -- Resolution level to pull and push data at. Defaults to 0, the highest resolution.

  • url_segments -- Precomputed path to segmentation data. Optional, default None.

  • fill_missing -- Always passes directly into 'CloudVolume()' function to fill missing segent/image values with 0s.

  • use_https -- Always passes directly into 'CloudVolume()' function to set use_https to the desired value.

url

CloudVolumePrecomputedPath to image data.

url_segments

CloudVolumePrecomputedPath to segmentation data. Optional, default None. Automatically tries precomputed path url+"_segments" if None.

cv

CloudVolume object for image data.

Type

CloudVolumePrecomputed

cv_segments

CloudVolume object for segmentation data. Optional, default None.

Type

CloudVolumePrecomputed

cv_annotations

CloudVolume object for segmentation data. Optional, default None.

Type

CloudVolumePrecomputed

mip

Resolution level.

chunk_size

The chunk size of the volume at the specified mip, given as (x, y, z).

scales

The resolution of the volume at the specified mip, given as (x, y, z).

class brainlit.utils.NeuronTrace(path: str, seg_id: int = None, mip: int = None, rounding: bool = True, read_offset: bool = False, fill_missing: bool = True, use_https: bool = False)[source]

Neuron Trace class to handle neuron traces as swcs and s3 skeletons

Parameters

  • path (str) -- Path to either s3 bucket (url) or swc file (filepath).

  • seg_id (int) -- If s3 bucket path is provided, the segment number to pull, default None.

  • mip (int) -- If s3 bucket path is provided, the resolution to use for scaling, default None.

  • rounding (bool) -- If s3 is provided, specifies if it should be rounded, default True

  • read_offset (bool) -- If swc is provided, whether offset should be read from file, default False.

  • fill_missing (bool) -- Always passes directly into 'CloudVolume()' function to fill missing skeleton values with 0s, default True.

  • use_https (bool) -- Always passes directly into 'CloudVolume()' function to set use_https to desired value, default True.

path

Path to either s3 bucket (url) or swc file (filepath)

Type

str

input_type

Specifies whether input file is 'swc' or 'skel'

Type

bool

df

Indices, coordinates, and parents of each node

Type

pandas.DataFrame

args

Stores arguments for df - offset, color, cc, branch

Type

tuple

seg_id

If s3 bucket path is provided, the segment number to pull

Type

int

mip

If s3 bucket path is provided, the resolution to use for scaling

Type

None,int

Example

>>> swc_path = "./data/data_octree/consensus-swcs/2018-08-01_G-002_consensus.swc"
>>> s3_path = "s3://open-neurodata/brainlit/brain1_segments"
>>> seg_id = 11
>>> mip = 2

>>> swc_trace = NeuronTrace(swc_path)
>>> s3_trace = NeuronTrace(s3_path,seg_id,mip)
brainlit.utils.czi_to_zarr(czi_path: str, out_dir: str, fg_channel: int = 0, parallel: int = 1)[source]

Convert 4D czi image to a zarr file(s) at a given directory. Single channel image will produce a single zarr, two channels will produce two.

Parameters

  • czi_path (str) -- Path to czi image.

  • out_dir (str) -- Path to directory where zarr(s) will be written.

  • fg_channel (int) -- Index of foreground channel.

  • parallel (int) -- Number of cpus to use to write zarr.

Returns

paths to zarrs that were written

Return type

list

brainlit.utils.zarr_to_omezarr(zarr_path: str, out_path: str, res: list)[source]

Convert 3D zarr to ome-zarr.

Parameters

  • zarr_path (str) -- Path to zarr.

  • out_path (str) -- Path of ome-zarr to be created.

  • res (list) -- List of xyz resolution values in nanometers.

Raises

S3 Helper Methods

brainlit.utils.get_data_ranges(bin_path: List[List[str]], chunk_size: Tuple[int, int, int])[source]

Get ranges (x,y,z) for chunks to be stitched together in volume

Parameters

  • bin_path -- Binary paths to files.

  • chunk_size -- The size of chunk to get ranges over.

Returns

x-coord int bounds. y_range: y-coord int bounds. z_range: z-coord int bounds.

Return type

x_range