Command line scripts¶

Automatic orientation of intensity image¶

Automatic orientation of object in images.

usage: orientation [-h] [--extra_channels EXTRA_CHANNELS [EXTRA_CHANNELS ...]]
                   [--regexp_channels REGEXP_CHANNELS]
                   [--out_suffix OUT_SUFFIX] [--format FORMAT]
                   [--output_path OUTPUT_PATH]
                   [--log_level {ERROR,WARNING,NOTSET,CRITICAL,DEBUG,INFO}]
                   images [images ...]

Positional Arguments¶

images: list of images filename to orient.

Extra channels options¶

--extra_channels: list of extra channels to orient, limit to one image as first argument!.
--regexp_channels: the position of the variable character in file names to define extra-channel.

output arguments¶

--out_suffix

suffix to add to the file prior to saving.

Default: “-auto_rotated”

--format

if specified, may change the output image format.

--output_path

if specified, change the output path.

logging arguments¶

--log_level

Possible choices: ERROR, WARNING, NOTSET, CRITICAL, DEBUG, INFO

logging level to use, ‘INFO’ by default.

Default: “INFO”

Orient the object along its main axes.

Image resampling¶

Resampling an image allow to change its voxelsize and shape using interpolation methods while preserving the image physical extent.

usage: resampling [-h] [--label | --linear] [-p OUTPUT_PATH] [-f FORMAT]
                  [-r REPLACE REPLACE]
                  [--log_level {ERROR,WARNING,NOTSET,CRITICAL,DEBUG,INFO}]
                  images [images ...] voxelsize [voxelsize ...]

Positional Arguments¶

images: image or list of images to resample.
voxelsize: voxelsize or list voxelsize for each axis.

Named Arguments¶

--label

use it to resample labelled images, change the interpolation method to ‘nearest’.

Default: False

--linear

use it with intensity images, change the interpolation method to ‘linear’ instead of ‘cubic-spline’.

Default: False

output arguments¶

-p, --output_path: if specified, change the output path. Make sure it is empty as it could overwrite the files!
-f, --format: if specified, change the output image format.
-r, --replace: if specified, replace the string in output image format.Should be made of two parts, the chain to replace and the replacement.

logging arguments¶

--log_level

Possible choices: ERROR, WARNING, NOTSET, CRITICAL, DEBUG, INFO

logging level to use, ‘INFO’ by default.

Default: “INFO”

Pay attention to the type of image you are interpolating, intensity or labelled, as it modify the information contained in the image depending on the selected method!

Multi-angle images manual landmarks definition¶

Manually place landmarks for multi-angles fusion initialisation.

usage: multiangle_initialisation [-h] [-d DATASET] [-t TIME_INDEX]
                                 [--channel CHANNEL] [-o OUT_DATASET]
                                 [--log_level {ERROR,WARNING,NOTSET,CRITICAL,DEBUG,INFO}]
                                 json

Positional Arguments¶

json: a JSON file containing the metadata and locations of the required dataset.

Named Arguments¶

-d, --dataset

the dataset to use as intensity image input for fusion algorithm, ‘raw’ by default.

Default: “raw”

-t, --time_index

the time-index of the multi-angles image used in fusion procedure, all of them by default.

Default: []

multichannel image arguments¶

--channel: channel to use with a multichannel image.

output arguments¶

-o, --out_dataset

the dataset name to use to save landmarks files, ‘multiangle_landmarks’ by default.

Default: “multiangle_landmarks”

logging arguments¶

--log_level

Possible choices: ERROR, WARNING, NOTSET, CRITICAL, DEBUG, INFO

logging level to use, ‘INFO’ by default

Default: “INFO”

Multi-angle images fusion¶

Performs multi-angle images registration and fusion

usage: multiangle_fusion [-h] [-d DATASET] [-t TIME_INDEX] [--manual_init]
                         [--n_iter N_ITER [N_ITER ...]]
                         [--average_method {mean,robust-mean,median,minimum,maximum,quantile,sum,var,stddev}]
                         [--super_resolution] [--global_averaging]
                         [--last_non_linear] [--py_ll PY_LL [PY_LL ...]]
                         [--channel CHANNEL] [--ext EXT]
                         [--out_dataset OUT_DATASET]
                         [--log_level {ERROR,WARNING,NOTSET,CRITICAL,DEBUG,INFO}]
                         json

Positional Arguments¶

json: a JSON file containing the metadata and locations of the required dataset.

Named Arguments¶

-d, --dataset

the dataset to use as intensity image input for multi-angles image fusion procedure, ‘raw’ by default.

Default: “raw”

-t, --time_index

the time-index of the multi-angles image used in fusion procedure, all of them by default.

Default: []

fusion arguments¶

--manual_init

add this option to use prior manual definition of landmarks with multiangle_initialisation.py.

Default: False

--n_iter

number of iterations to performs when fusing multi-angle images, default is 2.

Default: 2

--average_method

Possible choices: mean, robust-mean, median, minimum, maximum, quantile, sum, var, stddev

averaging method to use when fusing multi-angle images, default is mean.

Default: [‘mean’, ‘robust-mean’, ‘median’, ‘minimum’, ‘maximum’, ‘quantile’, ‘sum’, ‘var’, ‘stddev’]

--super_resolution

creates a super-resolution image when fusing multi-angle images at last step.

Default: False

--global_averaging

perform global averaging of each voxel by the total number of images, else use mask for local averaging.

Default: False

--last_non_linear

perform non-linear registration at last iteration step, else only rigid and affine registrations are used.

Default: False

--py_ll

use this to control the pyramid lowest level for block-matching, 2 by default.

Default: 2

multichannel image arguments¶

--channel: channel to use with a multichannel image.

output arguments¶

--ext

extension used to save fused images, ‘tif’ by default.

Default: “tif”

--out_dataset

export fused images in a ‘fusion’ dataset.

Default: “fusion”

logging arguments¶

--log_level

Possible choices: ERROR, WARNING, NOTSET, CRITICAL, DEBUG, INFO

logging level to use, ‘INFO’ by default.

Default: “INFO”

Sequence registration¶

Sequence registration of a time-series.

Sequence registration is a (temporal) forward registration of all images of a time series onto the last one. Use image I[t] (image at time t) as float and image I[N] as reference, with N the index of the last image of the temporal sequence. It allows to obtain a sequence fully registered on the same template, i.e. same image frame (shape, extent, …).

This tool will produce the following data:

a series of sequence transformations allowing registration of I[t] onto I[N] frame (saved under the trsf_dataset location).

a series of sequence registered images, that is I[t] registered onto I[N] frame (saved under the out_dataset location).

This tool will produce the following figure:

a set of “original” projections for the time-series

a set of “registered” projections for the time-series

Note that the “rigid” part of the transformations is always saved. Except for the figures, the produced data is automatically referenced in the JSON file.

usage: sequence_registration [-h] [-int INTENSITY_DATASET]
                             [-seg SEGMENTATION_DATASET] [-trsf TRSF_DATASET]
                             [--channel CHANNEL] [--orientation {1,-1}]
                             [--registration_type {similitude,rigid,affine,vectorfield}]
                             [--proj_method {contour,background,maximum,average,minimum,max,mean,min}]
                             [--ext EXT] [--out_dataset OUT_DATASET] [--force]
                             [--log_level {ERROR,WARNING,NOTSET,CRITICAL,DEBUG,INFO}]
                             json

Positional Arguments¶

json: a JSON file containing the metadata and locations of the required dataset.

Named Arguments¶

-int, --intensity_dataset

name of the dataset containing the intensity images, ‘raw’ by default.

Default: “raw”

-seg, --segmentation_dataset

the dataset containing the segmented image on which to project the dataset, ‘watershed_segmentation’ by default.

Default: “watershed_segmentation”

-trsf, --trsf_dataset

name of the dataset containing the transformations, ‘trsf’ by default.

Default: “trsf”

images arguments¶

--channel

channel to register, mandatory for multichannel images.

--orientation

Possible choices: 1, -1

image orientation, use -1 with an inverted microscope, 1 by default.

Default: 1

registration arguments¶

--registration_type

Possible choices: similitude, rigid, affine, vectorfield

type of registration to performs, ‘rigid’ by default.

Default: “rigid”

--force

force computation of transformations.

Default: False

figure arguments¶

--proj_method

Possible choices: contour, background, maximum, average, minimum, max, mean, min

projection method to use. ‘contour’ (default) works well with cell walls/membranes. ‘maximum’ works well with nuclei.

Default: “contour”

output arguments¶

--ext

file extension of registered images, ‘tif’ by default.

Default: “tif”

--out_dataset

export images in ‘temporal_registration’ dataset

Default: “temporal_registration”

logging arguments¶

--log_level

Possible choices: ERROR, WARNING, NOTSET, CRITICAL, DEBUG, INFO

logging level to use, ‘INFO’ by default.

Default: “INFO”

Table of Contents

Command line scripts¶

Automatic orientation of intensity image¶

Positional Arguments¶

Extra channels options¶

output arguments¶

logging arguments¶

Image resampling¶

Positional Arguments¶

Named Arguments¶

output arguments¶

logging arguments¶

Multi-angle images manual landmarks definition¶

Positional Arguments¶

Named Arguments¶

multichannel image arguments¶

output arguments¶

logging arguments¶

Multi-angle images fusion¶

Positional Arguments¶

Named Arguments¶

fusion arguments¶

multichannel image arguments¶

output arguments¶

logging arguments¶

Sequence registration¶

Positional Arguments¶

Named Arguments¶

images arguments¶

registration arguments¶

figure arguments¶

output arguments¶

logging arguments¶

Temporal projection¶