config

Qiber3D.config.app_author = 'Anna Jaeschke; Hagen Eckert'

str: Authors

Qiber3D.config.app_name = 'Qiber3D'

Name of the app

Qiber3D.config.core_count = 0

int: CPU core count (0 = autodetect)

class Qiber3D.config.extract

Bases: object

Parameter to extract a Qiber3D.Network from an image stack

class binary

Bases: object

Binarization

threshold = 'Otsu'

(float or string): binarization threshold in percent, or name of the following auto threshold methods - Otsu, Isodata, Li, Mean, Minimum, Triangle, Yen (examples)

invert = False

bool: invert the input image (extracted structures should be high and background low)

class isotropic_resampling

Bases: object

Rescaling to cubic voxels

target = 'z'

string: select if the z resolution or the xy resolution should be adjust to form cubic voxels

low_memory = False

bool: reduce the memory footprint by using less precision when possible

class median

Bases: object

Median filter - despeckle

apply = True

bool: apply the median filter to the image

footprint = None

array: If set, this 3D binary array is used instead of the size parameter to describe the neighborhood

size = 3

(int or array): size of the neighborhood cuboid, if an int is given the all three axis have the same length

class morph

Bases: object

Morphological dilation and erosion

apply = True

bool: apply the dilation and erosion to the image

iterations = 5

int: number of iterations

remove_vol = 100

float: remove islands with volume smaller than volume smaller than remove_vol - in (voxel_size units)^3

nd2_channel_name = 0

str or int: channel name or index when importing from nd2 files

save_steps = True

bool: save extraction steps compressed in memory

class smooth

Bases: object

Gaussian filter

apply = True

bool: apply a gaussian filter and erosion to the image

sigma = 2.0

float: standard deviation for Gaussian kernel in voxel

truncate = 2.0

float: truncate the filter after this many standard deviations

class teasar

Bases: object

TEASER reconstruction - for parameter explanation see kimimaro

const = 0

dust_threshold = 600

max_paths = 50

pdrf_exponent = 4

pdrf_scale = 100000

scale = 1

soma_acceptance_threshold = 3500

soma_detection_threshold = 1100

soma_invalidation_const = 300

soma_invalidation_scale = 1.0

class thinning

Bases: object

Thinning based reconstruction

distance_voxel_overlap = 15

int: Overlap in voxel for the low memory euclidean distance transformation

sliver_threshold = 6

int: segments with less than sliver_threshold voxels will be treated specially (minimum of 6)

voxel_per_point = 10

float: distance between interpolated points (every segment will have at least five points)

use_teasar = False

bool: if True use the kimimaro TEASAR implementation for reconstruction

voxel_size = None

list(float): size of a voxel in each axis

class z_drop

Bases: object

Z-Drop - Intensity attenuation correction

apply = True

bool: apply the intensity attenuation correction to the image

class Qiber3D.config.figure

Bases: object

Settings for matplotlib based figures

dpi = 300

int: figure resolution

format = '.pdf'

str: default figure export format

grid_color = (0.2, 0.2, 0.2)

tuple(float): grid rgb color tuple for directions figure

grid_lw = 0.25

float: grid line width for directions figure

Qiber3D.config.log_level = 20

int: default logging level. Use Qiber3D.helper.change_log_level() to change it on the fly

class Qiber3D.config.render

Bases: object

Settings for rendering images and animations

animation_height = 720

int: vertical resolution for animations

background = (0.0, 0.0, 0.0)

tuple(float): background color as RGB values (0-1)

color = (0.9, 0.2, 0.2)

tuple(floats): standard foreground color

ffmpeg_path = 'ffmpeg'

str: path to local installation of ffmpeg

image_resolution = 3840

int: horizontal resolution for images

notebook = False

bool: switch to adapt render pipeline for jupyter notebooks (automatically set)

rgba = True

bool: allow transparency for images

Qiber3D.config.url = 'https://github.com/theia-dev/Qiber3D'

str: git url

Qiber3D.config.version = '0.7.0'

str: version

Qiber3D.config.version_number = (0, 7, 0)

tuple(int): version number