palmari.image_tools package

Submodules

palmari.image_tools.cell_mask module

palmari.image_tools.cell_mask.get_cell_mask(data: numpy.ndarray)

palmari.image_tools.cell_mask.tag_localizations_per_cell(pos: pandas.core.frame.DataFrame, labels: numpy.ndarray, scale: float)

palmari.image_tools.correct_drift module

palmari.image_tools.correct_drift.correct_drift(pos, L=0.2, step_size=0.03, prog_bar_position=None, min_n_locs_per_bin: int = 10000, max_n_bins: int = 20)

palmari.image_tools.correct_drift.get_optimal_shift(pos1, pos2, L, step)

palmari.image_tools.density_filtering module

palmari.image_tools.density_filtering.density_filtering(pos: pandas.core.frame.DataFrame, radius: float = 0.2, n_neighbors: Optional[int] = None) → pandas.core.series.Series

palmari.image_tools.intensity module

palmari.image_tools.intensity.mean_intensity_center(data)

palmari.image_tools.intensity.smooth_average(x, w)

palmari.image_tools.localization module

palmari.image_tools.localization.SMLM_filtering(data, filter_size, scale)

palmari.image_tools.localization.SMLM_localization(data: numpy.ndarray, factor: float = 1.0, filter_size: int = 3, scale: float = 2.0, verbose: bool = False, return_all: bool = False, subpixel_mode: str = 'radial', frame_start: int = 0)

palmari.image_tools.localization.b_splines(x, scale, order)

palmari.image_tools.localization.lsradialcenterfit(m, b, w)

Adapted from Matlab code found in https://www.nature.com/articles/nmeth.2071 Least squares solution to determine the radial symmetry center. Inputs m, b, w are defined on a grid. w are the weights for each point.

palmari.image_tools.localization.make_filters(scale, order, L)

palmari.image_tools.localization.phaser(ROI: numpy.array)

Adapted from https://colab.research.google.com/drive/1Jir3HxTZ-au8L56ZrNHGxfBD0XlDkOMl

Parameters

ROI (np.array) – 2D array on which to run the dubpixel localization.

Returns

x, y, sigma. in pixels.

Return type

tuple

palmari.image_tools.localization.plus_func(x, n)

palmari.image_tools.localization.radialCenter(I)

palmari.image_tools.localization.sliding_window_filter(data: dask.array.core.Array, percentile: float = 10, window_size: int = 100)

Module contents