neuralib.scanbox.view.ScanBoxView

class neuralib.scanbox.view.ScanBoxView

Bases: object

Scanbox info and data

Dimension parameters:

F = number of frames

P = number of optical planes

C = number of PMT channels

W = FOV width

H = FOV height

__init__(directory)

Parameters:

directory (str | Path | PathLike[str]) – directory contain .sbx & .mat files

Methods

__init__(directory)
show(frames, plane, channel)	play the selected frames using customized CV2 player
to_tiff(frames, plane, channel, output)	Convert the selected frames to tiff file

Attributes

height	fov height
meta	scanbox meta information
n_channels	sbx issue, a bit of hard-coded
n_frames	number of frames per plane
n_planes	number of optical imaging planes
version	scanbox version
width	fov width
info	SBXInfo
sbx_map	Array[float, [F, P, C, W, H]]

__init__(directory)

Parameters:

directory (str | Path | PathLike[str]) – directory contain .sbx & .mat files

sbx_map: sbx_memmap

Array[float, [F, P, C, W, H]]

info: SBXInfo

SBXInfo

property meta: dict[str, Any]

scanbox meta information

property version: int

scanbox version

property height: int

fov height

property width: int

fov width

property n_planes: int

number of optical imaging planes

property n_channels: int

sbx issue, a bit of hard-coded

property n_frames: int

number of frames per plane

show(frames, plane, channel)

play the selected frames using customized CV2 player

Parameters:

• frames (slice | ndarray | None) – selected frames. If None, play all sequences

• plane (int) – number of optical planes

• channel (int) – number of PMT channel

to_tiff(frames, plane, channel, output)

Convert the selected frames to tiff file

Parameters:

• frames (slice | ndarray | None) – selected frames. If None, convert all sequences

• plane (int) – number of optical planes

• channel (int) – number of PMT channel

• output (str | Path | PathLike[str]) – output filename