roiextractors.example_datasets package

Submodules

roiextractors.example_datasets.toy_example module

Toy example ImagingExtractor and SegmentationExtractor for testing.

Functions

toy_example

Create a toy example of an ImagingExtractor and a SegmentationExtractor.

_gaussian(x, mu, sigma)

Compute classical gaussian with parameters x, mu, sigma.

_generate_rois(num_units=10, size_x=100, size_y=100, roi_size=4, min_dist=5, mode='uniform')

Generate ROIs with given parameters.

Parameters:

• num_units (int) – Number of ROIs

• size_x (int) – Size of x dimension (pixels)

• size_y (int) – Size of y dimension (pixels)

• roi_size (int) – Siz of ROI in x and y dimension (pixels)

• min_dist (int) – Minimum distance between ROI centers (pixels)

• mode (str) – ‘uniform’ or ‘gaussian’. If ‘uniform’, ROI values are uniform and equal to 1. If ‘gaussian’, ROI values are gaussian modulated

Returns:

• roi_pixels (list) – List of pixel coordinates for each ROI

• image (np.ndarray) – Image with ROIs

• means (list) – List of mean coordinates for each ROI

toy_example(duration=10, num_rois=10, size_x=100, size_y=100, roi_size=4, min_dist=5, mode='uniform', sampling_frequency=30.0, decay_time=0.5, noise_std=0.05)

Create a toy example of an ImagingExtractor and a SegmentationExtractor.

Parameters:

• duration (float) – Duration in s

• num_rois (int) – Number of ROIs

• size_x (int) – Size of x dimension (pixels)

• size_y (int) – Size of y dimension (pixels)

• roi_size (int) – Size of ROI in x and y dimension (pixels)

• min_dist (int) – Minimum distance between ROI centers (pixels)

• mode (str) – ‘uniform’ or ‘gaussian’. If ‘uniform’, ROI values are uniform and equal to 1. If ‘gaussian’, ROI values are gaussian modulated

• sampling_frequency (float) – The sampling rate

• decay_time (float) – Decay time of fluorescence reponse

• noise_std (float) – Standard deviation of added gaussian noise

Returns:

• imag (NumpyImagingExtractor) – The output imaging extractor

• seg (NumpySegmentationExtractor) – The output segmentation extractor

Module contents

Toy example ImagingExtractor and SegmentationExtractor for testing.

Modules

toy_example

Create a toy example of an ImagingExtractor and a SegmentationExtractor.

Functions

toy_example

Create a toy example of an ImagingExtractor and a SegmentationExtractor.