{"id":13717137,"url":"https://github.com/rraadd88/htsimaging","last_synced_at":"2025-06-22T02:33:15.786Z","repository":{"id":64273359,"uuid":"52201279","full_name":"rraadd88/htsimaging","owner":"rraadd88","description":"🔬Python package for high-throughput single-cell imaging 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imaging"],"sub_categories":[],"readme":"\u003c!-- PROJECT SHIELDS --\u003e\n\u003cdiv align=\"center\"\u003e\n  \n\u003c!-- [![Contributors][contributors-shield]][contributors-url]\n[![Forks][forks-shield]][forks-url]\n[![Stargazers][stars-shield]][stars-url] --\u003e\n\u003ca href=\"\"\u003e[![PyPI](https://img.shields.io/pypi/v/htsimaging?style=for-the-badge)![Python](https://img.shields.io/pypi/pyversions/htsimaging?style=for-the-badge)](https://pypi.org/project/htsimaging)\u003c/a\u003e\n\u003ca href=\"\"\u003e[![build](https://img.shields.io/github/actions/workflow/status/rraadd88/htsimaging/build.yml?style=for-the-badge)](https://github.com/rraadd88/htsimaging/actions/workflows/build.yml)\u003c/a\u003e\n\u003ca href=\"\"\u003e[![Issues](https://img.shields.io/github/issues/rraadd88/htsimaging.svg?style=for-the-badge)](https://github.com/rraadd88/htsimaging/issues)\u003c/a\u003e\n\u003cbr /\u003e\n\u003ca href=\"\"\u003e[![Downloads](https://img.shields.io/pypi/dm/htsimaging?style=for-the-badge)](https://pepy.tech/project/htsimaging)\u003c/a\u003e\n\u003ca href=\"\"\u003e[![GNU License](https://img.shields.io/github/license/rraadd88/htsimaging.svg?style=for-the-badge)](https://github.com/rraadd88/htsimaging/blob/main/LICENSE)\u003c/a\u003e\n\u003c/div\u003e\n  \n\u003c!-- PROJECT LOGO --\u003e\n\u003cdiv align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/rraadd88/htsimaging/assets/9945034/66107572-ef49-4852-a228-f6b6aa9b42c8\" alt=\"logo\" /\u003e\n  \u003ch1 align=\"center\"\u003ehtsimaging\u003c/h1\u003e\n  \u003cp align=\"center\"\u003e\n    High-Throughput Single-cell Imaging analysis.\n    \u003cbr /\u003e\n    \u003ca href=\"https://github.com/rraadd88/htsimaging#examples\"\u003eExamples\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/rraadd88/htsimaging#api\"\u003eExplore the API\u003c/a\u003e\n  \u003c/p\u003e\n\u003c/div\u003e  \n\n![image](./examples/image.png)   \n\n# Examples  \n\n[📈 Single-cell protein abundance and its normalization](https://github.com/rraadd88/htsimaging/blob/main/examples/protein_abundance_and_normalization.ipynb)   \n[📈 Single-cell protein abundance by marker localization](https://github.com/rraadd88/htsimaging/blob/main/examples/protein_abundance_by_marker_location.ipynb)  \n[🖼️ Visualization of the images.](https://github.com/rraadd88/htsimaging/blob/main/examples/viz_image.ipynb)  \n[📈 Quantitative analysis of endocytosis.](https://github.com/rraadd88/htsimaging/blob/main/examples/endocytosis.ipynb)  \n[📈 Single-particle tracking (SPT).](https://github.com/rraadd88/htsimaging/blob/main/examples/spt.ipynb)  \n[📈 Calculating the recovery rate from a bleach-chase data](https://github.com/rraadd88/htsimaging/blob/main/examples/bleach_chase.ipynb)  \n\n# Installation\n    \n```\npip install htsimaging              # with basic dependencies  \n```\nWith additional dependencies as required:\n```\npip install htsimaging[spt]         # for the analysis of the Single-Particle Tracking e.g. endocytosis.\n```\n  \n# How to cite?  \n1. Using BibTeX:   \n```\n@software{Dandage_htsimaging,\n  title   = {htsimaging: High-Throughput Single-cell Imaging analysis in python},\n  author  = {Dandage, Rohan},\n  year    = {2023},\n  url     = {https://zenodo.org/doi/10.5281/zenodo.3697134},\n  version = {v1.0.5},\n  note    = {The URL is a DOI link to the permanent archive of the software.},\n}\n```\n2. DOI link: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3697134.svg)](https://zenodo.org/doi/10.5281/zenodo.3697134), or  \n\n3. Using citation information from [CITATION.CFF file](https://github.com/rraadd88/htsimaging/blob/main/CITATION.cff).  \n  \n\n# Future directions, for which contributions are welcome  \n- [ ] Command-line usage.  \n  \n# Similar projects  \n- https://github.com/vanvalenlab/deepcell-tf  \n- https://github.com/junlabucsd/napari-mm3  \n\n# API\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/bleach_chase\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.bleach_chase`\n\n\n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/bleach_chase.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.bleach_chase.stat`\nStatistical analysis of the bleach-chase \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/bleach_chase/stat.py#L5\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `exp1`\n\n```python\nexp1(x, lag, amplitude, rate)\n```\n\nOne-term exponential. \n\n\n\n**Parameters:**\n \n - \u003cb\u003e`x`\u003c/b\u003e (list):  input vector \n - \u003cb\u003e`lag`\u003c/b\u003e (float):  lag    \n - \u003cb\u003e`amplitude`\u003c/b\u003e (float):  amplitude \n - \u003cb\u003e`rate`\u003c/b\u003e (float):  rate \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/bleach_chase/stat.py#L16\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_scores`\n\n```python\nget_scores(df: DataFrame) → DataFrame\n```\n\nCalculate the rates other parameters. \n\n\n\n**Parameters:**\n \n - \u003cb\u003e`df`\u003c/b\u003e (pd.DataFrame):  input table. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  table with the parameters. \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.endocytosis.io`\nProcessing of the paths of input images to create configurations and metadata. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/io.py#L12\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `make_project_cfg`\n\n```python\nmake_project_cfg(\n    prjd: str,\n    output_dir_path: str,\n    bright_fn_marker: str = None,\n    segmented_fn_marker: str = None,\n    magnification: int = None,\n    image_ext: str = 'tif',\n    cores: int = 1,\n    test: bool = False,\n    force: bool = False\n) → dict\n```\n\nMake the confguration for the analysis run. \n\n\n\n**Args:**\n \n - \u003cb\u003e`prjd`\u003c/b\u003e (str):  path to the directory with the images. \n - \u003cb\u003e`output_dir_path`\u003c/b\u003e (str):  output directory path. \n - \u003cb\u003e`bright_fn_marker`\u003c/b\u003e (_type_):  marker in the path of the bright field images. \n - \u003cb\u003e`segmented_fn_marker`\u003c/b\u003e (_type_):  marker in the path of the segmented images. \n - \u003cb\u003e`cores`\u003c/b\u003e (int, optional):  number of cores. Defaults to 1. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test-mode. Defaults to False. \n - \u003cb\u003e`force`\u003c/b\u003e (bool, optional):  over-write theoutputs. Defaults to False. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`dict`\u003c/b\u003e:  metadata \n\n\n\n**Notes:**\n\n\u003e Infer the magnification from the filenames: if 'T1C1' in cfg['bright_fn_marker']: cfg['magnification']=150 elif cfg['bright_fn_marker']=='_t': cfg['magnification']=100 \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/io.py#L101\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `make_cell_cfg`\n\n```python\nmake_cell_cfg(\n    cfg: dict,\n    frames: list,\n    cells: list,\n    trial: str,\n    celli: int,\n    cellbox: list,\n    params_get_signal_summary_by_roi: dict = {'xy_center': None, 'width': 20, 'fun_summary_frame': 'min', 'fun_summary_frames': 'median'},\n    filterby_centroid: bool = False,\n    scale_signal_cytoplasm: float = 1.5,\n    test: bool = False,\n    force: bool = False\n) → dict\n```\n\nMake the configuration for an individual cell. \n\n\n\n**Args:**\n \n - \u003cb\u003e`cfg`\u003c/b\u003e (dict):  metadata. \n - \u003cb\u003e`frames`\u003c/b\u003e (list):  list of frames. \n - \u003cb\u003e`cells`\u003c/b\u003e (list):  list of cells. \n - \u003cb\u003e`trial`\u003c/b\u003e (str):  trial name. \n - \u003cb\u003e`celli`\u003c/b\u003e (int):  index of the cell. \n - \u003cb\u003e`cellbox`\u003c/b\u003e (list):  bounding box of the cell \n - \u003cb\u003e`params_get_signal_summary_by_roi`\u003c/b\u003e (dict, optional):  parameters for the aggregation of the values at the ROI. Defaults to {'xy_center':None,'width':20, 'fun_summary_frame':'min', 'fun_summary_frames':'median' }. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test-mode. Defaults to False. \n - \u003cb\u003e`force`\u003c/b\u003e (bool, optional):  over-write the output. Defaults to False. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`dict`\u003c/b\u003e:  metadata \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.endocytosis`\n\n\n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.endocytosis.vid`\nTo make the video of the timelapse images. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/vid.py#L9\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `make_gif`\n\n```python\nmake_gif(\n    cellcfg=None,\n    frames: list = None,\n    t_cor: DataFrame = None,\n    img_bright=None,\n    outd: str = None,\n    particle2color: dict = None,\n    test: bool = False,\n    force: bool = False\n)\n```\n\nMake a .gif file out of frames.  \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.endocytosis.viz`\nVisualizations. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/viz.py#L8\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `plot_properties_cell`\n\n```python\nplot_properties_cell(cellcfg, df2, cols_colorby, colx='x', coly='y')\n```\n\nPlot properties of the cell. \n\n\n\n**Args:**\n \n - \u003cb\u003e`cellcfg`\u003c/b\u003e (_type_):  config of a cell. \n - \u003cb\u003e`df2`\u003c/b\u003e (_type_):  input dataframe. \n - \u003cb\u003e`cols_colorby`\u003c/b\u003e (_type_):  columns to color by. \n - \u003cb\u003e`colx`\u003c/b\u003e (str, optional):  column with the x values. Defaults to 'x'. \n - \u003cb\u003e`coly`\u003c/b\u003e (str, optional):  column with the y values. Defaults to 'y'. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/viz.py#L52\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `image_locate_particles`\n\n```python\nimage_locate_particles(\n    df1: DataFrame,\n    frame,\n    img_region,\n    annotate_particles: str = False,\n    fig=None,\n    ax: Axes = None\n) → Axes\n```\n\nPlot image with particles. \n\n\n\n**Args:**\n \n - \u003cb\u003e`df1`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n - \u003cb\u003e`frame`\u003c/b\u003e (_type_):  image frame. \n - \u003cb\u003e`img_region`\u003c/b\u003e (_type_):  regions in the image. \n - \u003cb\u003e`annotate_particles`\u003c/b\u003e (str, optional):  annotate the paticles or not. Defaults to False. \n - \u003cb\u003e`fig`\u003c/b\u003e (_type_, optional):  figure object. Defaults to None. \n - \u003cb\u003e`ax`\u003c/b\u003e (plt.Axes, optional):  subplot object. Defaults to None. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`plt.Axes`\u003c/b\u003e:  _description_ \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/viz.py#L84\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `image_trajectories`\n\n```python\nimage_trajectories(\n    dtraj: DataFrame,\n    img_gfp=None,\n    img_bright=None,\n    label: bool = True,\n    fig=None,\n    ax: Axes = None\n) → Axes\n```\n\nPlot trajectories. \n\n\n\n**Args:**\n \n - \u003cb\u003e`dtraj`\u003c/b\u003e (pd.DataFrame):  input dataframe with the trajectories. \n - \u003cb\u003e`img_gfp`\u003c/b\u003e (_type_, optional):  channel image e.g. GFP. Defaults to None. \n - \u003cb\u003e`img_bright`\u003c/b\u003e (_type_, optional):  segmentation image e.g. bright field. Defaults to None. \n - \u003cb\u003e`label`\u003c/b\u003e (bool, optional):  label. Defaults to True. \n - \u003cb\u003e`fig`\u003c/b\u003e (_type_, optional):  figure object. Defaults to None. \n - \u003cb\u003e`ax`\u003c/b\u003e (plt.Axes, optional):  subplot object. Defaults to None. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`plt.Axes`\u003c/b\u003e:  subplot \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/endocytosis/viz.py#L124\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `plot_moving_particles`\n\n```python\nplot_moving_particles(\n    t_cor: DataFrame,\n    img_bright=None,\n    frame=None,\n    framei: int = 0,\n    particle2color=None,\n    test: bool = False,\n    outd: str = None\n)\n```\n\nPlot moving particles. \n\n\n\n**Args:**\n \n - \u003cb\u003e`t_cor`\u003c/b\u003e (pd.DataFrame):  input table \n - \u003cb\u003e`img_bright`\u003c/b\u003e (_type_, optional):  segmentation raw image (e.g. bright field). Defaults to None. \n - \u003cb\u003e`frame`\u003c/b\u003e (_type_, optional):  image frame. Defaults to None. \n - \u003cb\u003e`framei`\u003c/b\u003e (int, optional):  image frame index. Defaults to 0. \n - \u003cb\u003e`particle2color`\u003c/b\u003e (_type_, optional):  particle-wise colors. Defaults to None. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test-mode. Defaults to False. \n - \u003cb\u003e`outd`\u003c/b\u003e (str, optional):  path to the output directory. Defaults to None. \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.lib.io`\nI/O \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/io.py#L15\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `read_image`\n\n```python\nread_image(imp: str)\n```\n\nRead image. \n\n\n\n**Args:**\n \n - \u003cb\u003e`imp`\u003c/b\u003e (str):  path to the image file. \n\n\n\n**Returns:**\n np.array \n\nTODOs:  For a tiff file: from skimage.external import tifffile \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/io.py#L41\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `arr2vid`\n\n```python\narr2vid(\n    arr_list: list,\n    regions: list,\n    kins_mean: float,\n    vid_fh: str,\n    xpixels: list,\n    ypixels: list,\n    dpi: int = 100\n) → str\n```\n\nFrom array to video. \n\n\n\n**Args:**\n \n - \u003cb\u003e`arr_list`\u003c/b\u003e (list):  list of frames. \n - \u003cb\u003e`regions`\u003c/b\u003e (list):  regions  \n - \u003cb\u003e`kins_mean`\u003c/b\u003e (float):  kinetics  \n - \u003cb\u003e`vid_fh`\u003c/b\u003e (str):  video file path \n - \u003cb\u003e`xpixels`\u003c/b\u003e (list):  pixels allong x-axis. \n - \u003cb\u003e`ypixels`\u003c/b\u003e (list):  pixels allong y-axis. \n - \u003cb\u003e`dpi`\u003c/b\u003e (int, optional):  DPI resolution. Defaults to 100. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`str`\u003c/b\u003e:  path of the video \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/io.py#L91\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `makevid`\n\n```python\nmakevid(\n    gfp_list_stb: list,\n    brf_list_stb: list,\n    cmap_gfp: str,\n    cmap_brf: str,\n    vid_fh: str,\n    conditionn: int = None,\n    interval=None,\n    dpi: int = 300\n) → str\n```\n\nConvert to a video. \n\n\n\n**Args:**\n \n - \u003cb\u003e`gfp_list_stb`\u003c/b\u003e (list):  channel (e.g. GFP) images.   \n - \u003cb\u003e`brf_list_stb`\u003c/b\u003e (list):  segmented (e.g. bright-field) images.  \n - \u003cb\u003e`cmap_gfp`\u003c/b\u003e (str):  colormap for the channel images. \n - \u003cb\u003e`cmap_brf`\u003c/b\u003e (str):  colormap for the segmented images. \n - \u003cb\u003e`vid_fh`\u003c/b\u003e (str):  path to the video file. \n - \u003cb\u003e`conditionn`\u003c/b\u003e (int, optional):  title. Defaults to None. \n - \u003cb\u003e`interval`\u003c/b\u003e (_type_, optional):  inerval of the frames. Defaults to None. \n - \u003cb\u003e`dpi`\u003c/b\u003e (int, optional):  DPI resolution. Defaults to 300. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`str`\u003c/b\u003e:  path to the video file. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/io.py#L136\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `nd2arr_list`\n\n```python\nnd2arr_list(nd_dh: str = None, nd_fns: list = [], nd_fh: str = None) → list\n```\n\nRaw image to list of arrays. \n\n\n\n**Args:**\n \n - \u003cb\u003e`nd_dh`\u003c/b\u003e (str, optional):  directory containing raw files e.g. nd2. Defaults to None. \n - \u003cb\u003e`nd_fns`\u003c/b\u003e (list, optional):  file names. Defaults to []. \n - \u003cb\u003e`nd_fh`\u003c/b\u003e (str, optional):  path to the files. Defaults to None. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  list of arrays \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/io.py#L166\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `to_csv`\n\n```python\nto_csv(\n    fh_xls='../test/test.xlsx',\n    nd2_dh='/media/Transcend/20160219_000356_267',\n    cores=16\n)\n```\n\nConvert nd2 files to csv using parallel processing. \n\n\n\n**Args:**\n \n - \u003cb\u003e`fh_xls`\u003c/b\u003e (str, optional):  metadata file. Defaults to '../test/test.xlsx'. \n - \u003cb\u003e`nd2_dh`\u003c/b\u003e (str, optional):  path of the directory containing raw images. Defaults to \"/media/Transcend/20160219_000356_267\". \n - \u003cb\u003e`cores`\u003c/b\u003e (int, optional):  number of cores. Defaults to 16. \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.lib`\n\n\n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.lib.stat`\nStatistics. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L10\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `power`\n\n```python\npower(x, A, B)\n```\n\npower law equation. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L13\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `power_residuals`\n\n```python\npower_residuals(p, y, x)\n```\n\nDeviations of data from fitted 4PL curve \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L18\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `power_peval`\n\n```python\npower_peval(x, p)\n```\n\nEvaluated value at x with current parameters. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L23\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `line`\n\n```python\nline(x, m, C)\n```\n\npower law equation. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L26\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `line_residuals`\n\n```python\nline_residuals(p, y, x)\n```\n\nDeviations of data from fitted 4PL curve \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L31\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `line_peval`\n\n```python\nline_peval(x, p)\n```\n\nEvaluated value at x with current parameters. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L36\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `logistic4`\n\n```python\nlogistic4(x, A, B, C, D)\n```\n\n\n\n\n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L38\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `logistic4_residuals`\n\n```python\nlogistic4_residuals(p, y, x)\n```\n\nDeviations of data from fitted 4PL curve \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L43\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `logistic4_peval`\n\n```python\nlogistic4_peval(x, p)\n```\n\nEvaluated value at x with current parameters. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L48\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `logistic5`\n\n```python\nlogistic5(x, A, B, C, D, E)\n```\n\n\n\n\n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L50\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `logistic5_residuals`\n\n```python\nlogistic5_residuals(p, y, x)\n```\n\nDeviations of data from fitted 4PL curve \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L55\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `logistic5_peval`\n\n```python\nlogistic5_peval(x, p)\n```\n\nEvaluated value at x with current parameters. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L60\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `fit_power`\n\n```python\nfit_power(x, y, p0: list = [0, 1], plot: bool = False)\n```\n\nFit power law. \n\n\n\n**Args:**\n \n - \u003cb\u003e`x`\u003c/b\u003e (vector-like):  x values. \n - \u003cb\u003e`y`\u003c/b\u003e (vector-like):  y values. \n - \u003cb\u003e`p0`\u003c/b\u003e (list, optional):  starting parameters. Defaults to [0, 1]. \n - \u003cb\u003e`plot`\u003c/b\u003e (bool, optional):  to plot or not. Defaults to False. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`tuple`\u003c/b\u003e:  outputs. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L89\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `fit_line`\n\n```python\nfit_line(x, y, p0: list = [0, 1], plot: bool = False) → tuple\n```\n\nFit power law. \n\n\n\n**Args:**\n \n - \u003cb\u003e`x`\u003c/b\u003e (vector-like):  x values. \n - \u003cb\u003e`y`\u003c/b\u003e (vector-like):  y values. \n - \u003cb\u003e`p0`\u003c/b\u003e (list, optional):  _description_. Defaults to [0, 1]. \n - \u003cb\u003e`plot`\u003c/b\u003e (bool, optional):  _description_. Defaults to False. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`tuple`\u003c/b\u003e:  outputs \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L118\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_slope`\n\n```python\nget_slope(df: DataFrame, ds: Series) → float\n```\n\nGet slope for a section of the line. \n\n\n\n**Args:**\n \n - \u003cb\u003e`df`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n - \u003cb\u003e`ds`\u003c/b\u003e (pd.Series):  section of the line. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`float`\u003c/b\u003e:  slope. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/stat.py#L135\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_inflection_point`\n\n```python\nget_inflection_point(df: DataFrame, threshold_slope: float = 0.25) → DataFrame\n```\n\nGet inflation point. \n\n\n\n**Args:**\n \n - \u003cb\u003e`df`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n - \u003cb\u003e`threshold_slope`\u003c/b\u003e (float, optional):  threshold on the slope. Defaults to 0.25. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.lib.utils`\nUtilities for the image processing. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L12\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `filterframe`\n\n```python\nfilterframe(frame, cutoff: float = 0)\n```\n\nFilter a frame. \n\n\n\n**Args:**\n \n - \u003cb\u003e`frame`\u003c/b\u003e (array-like):  input frame. \n - \u003cb\u003e`cutoff`\u003c/b\u003e (float, optional):  cutoff on the values. Defaults to 0. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`array-like`\u003c/b\u003e:  filtered frame. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L30\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `filterframes`\n\n```python\nfilterframes(frames: list, cutoff: float = 0) → list\n```\n\nFilter the frames. \n\n\n\n**Args:**\n \n - \u003cb\u003e`frames`\u003c/b\u003e (list):  list of frames. \n - \u003cb\u003e`cutoff`\u003c/b\u003e (float, optional):  threshold on the values. Defaults to 0. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  list of frames. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L48\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_data_by_regions`\n\n```python\nget_data_by_regions(\n    regions: list,\n    img=None,\n    prop_type: str = 'area'\n) → DataFrame\n```\n\nGet properties by regions. \n\n\n\n**Args:**\n \n - \u003cb\u003e`regions`\u003c/b\u003e (list):  list of the regions. \n - \u003cb\u003e`img`\u003c/b\u003e (array-like, optional):  input image. Defaults to None. \n - \u003cb\u003e`prop_type`\u003c/b\u003e (str, optional):  property type. Defaults to 'area'. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L74\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `filter_regions`\n\n```python\nfilter_regions(\n    regions: list,\n    kind='labeled',\n    img=None,\n    prop_type: str = 'area',\n    mn: float = 0,\n    mx: float = 0,\n    test: bool = False,\n    plotp: str = None\n) → list\n```\n\nFilter regions. \n\n\n\n**Args:**\n \n - \u003cb\u003e`regions`\u003c/b\u003e (np.array):  segmented image, labeled with `measure.label(regions)`. \n - \u003cb\u003e`img`\u003c/b\u003e (array-like, optional):  image. Defaults to None. \n - \u003cb\u003e`prop_type`\u003c/b\u003e (str, optional):  property type. Defaults to 'area'. \n - \u003cb\u003e`mn`\u003c/b\u003e (float, optional):  minimum value. Defaults to 0. \n - \u003cb\u003e`mx`\u003c/b\u003e (float, optional):  maximum value. Defaults to 0. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test the filtering. Defaults to False. \n - \u003cb\u003e`plotp`\u003c/b\u003e (str, optional):  path to the plot. Defaults to None. \n\n\n\n**Raises:**\n \n - \u003cb\u003e`ValueError`\u003c/b\u003e:  img is required if filtering is t be done by the intensity. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  list of the filtered regions. \n\n\n\n**Notes:**\n\n\u003e Prefer `regionprops_table` which is new in sklean's version 0.16. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L144\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `smoothen`\n\n```python\nsmoothen(img)\n```\n\nSmoothen the image. \n\n\n\n**Args:**\n \n - \u003cb\u003e`img`\u003c/b\u003e (array-like):  input image. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`array-like`\u003c/b\u003e:  output image \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L159\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `smoothenframes`\n\n```python\nsmoothenframes(frames: list) → list\n```\n\nSmoothen the images. \n\n\n\n**Args:**\n \n - \u003cb\u003e`frames`\u003c/b\u003e (list):  list of frames. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  list of frames. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L175\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_regions`\n\n```python\nget_regions(img)\n```\n\nGet regions. \n\n\n\n**Args:**\n \n - \u003cb\u003e`img`\u003c/b\u003e (array-like):  input image \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L199\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `raw2phasecorr`\n\n```python\nraw2phasecorr(arr_list: list, clip: int = 0) → list\n```\n\nCorrect for the relative translative offset by phase correlation between images. \n\n\n\n**Args:**\n \n - \u003cb\u003e`arr_list`\u003c/b\u003e (list):  list of frames. \n - \u003cb\u003e`clip`\u003c/b\u003e (int, optional):  threshold. Defaults to 0. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  output frames. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L238\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `phasecorr_with`\n\n```python\nphasecorr_with(imlist: list, imlist2: list = None, clip: int = 0)\n```\n\nCorrect for the relative translative offset by phase correlation with a set of given images.  \n\n\n\n**Args:**\n \n - \u003cb\u003e`imlist`\u003c/b\u003e (list):  test images \n - \u003cb\u003e`imlist2`\u003c/b\u003e (list, optional):  reference images. Defaults to None. \n - \u003cb\u003e`clip`\u003c/b\u003e (int, optional):  threshold. Defaults to 0. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  corrected images. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L285\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `imlistcropper`\n\n```python\nimlistcropper(imlist: list, loci: int) → list\n```\n\nCrop a list of images. \n\n\n\n**Args:**\n \n - \u003cb\u003e`imlist`\u003c/b\u003e (list):  list of images. \n - \u003cb\u003e`loci`\u003c/b\u003e (int):  locations. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  output images. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L306\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `imclipper`\n\n```python\nimclipper(im_stb, clip: float)\n```\n\nCrop an image. \n\n\n\n**Args:**\n \n - \u003cb\u003e`im_stb`\u003c/b\u003e (array-like):  input image \n - \u003cb\u003e`clip`\u003c/b\u003e (float):  threshold. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L326\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_cellprops`\n\n```python\nget_cellprops(\n    regions,\n    intensity_imgtype2img,\n    properties=['area', 'bbox_area', 'convex_area', 'eccentricity', 'equivalent_diameter', 'euler_number', 'extent', 'filled_area', 'label', 'major_axis_length', 'max_intensity', 'mean_intensity', 'min_intensity', 'minor_axis_length', 'orientation', 'perimeter', 'solidity', 'centroid']\n) → DataFrame\n```\n\nGet cell properties. \n\n\n\n**Args:**\n \n - \u003cb\u003e`regions`\u003c/b\u003e (list):  regions in a frame. \n - \u003cb\u003e`intensity_imgtype2img`\u003c/b\u003e (_type_):  intensities. \n - \u003cb\u003e`properties`\u003c/b\u003e (list, optional):  _description_. Defaults to ['area', 'bbox_area', 'convex_area', 'eccentricity', 'equivalent_diameter', 'euler_number', 'extent', 'filled_area', 'label', 'major_axis_length', 'max_intensity', 'mean_intensity', 'min_intensity', 'minor_axis_length', 'orientation', 'perimeter', 'solidity', 'centroid', ]. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/lib/utils.py#L370\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_signal_summary_by_roi`\n\n```python\nget_signal_summary_by_roi(\n    cellframes: list,\n    xy_center: tuple = None,\n    width: int = 20,\n    fun_summary_frame: str = 'min',\n    fun_summary_frames: str = 'median'\n)\n```\n\nPlace of the roi in the image is defined by \n\n\n\n**Args:**\n \n - \u003cb\u003e`cellframes`\u003c/b\u003e (list):  list of frames. \n - \u003cb\u003e`xy_center`\u003c/b\u003e (tuple, optional):  position of the center. Defaults to None. \n - \u003cb\u003e`width`\u003c/b\u003e (int, optional):  width of the ROI. Defaults to 20. \n - \u003cb\u003e`fun_summary_frame`\u003c/b\u003e (str, optional):  function to summarise a frame. Defaults to 'min'. \n - \u003cb\u003e`fun_summary_frames`\u003c/b\u003e (str, optional):  function to summarise a list of frames. Defaults to 'median'. \n\n\n\n**Returns:**\n summary value \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/segment\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.segment`\n\n\n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/segment.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.segment.region`\nProcessing of the segmented regions. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/segment/region.py#L11\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `segmentation2cells`\n\n```python\nsegmentation2cells(\n    imsegp: str,\n    kind: str = 'yeast',\n    fiterby_border_thickness: int = None,\n    magnification: int = 100,\n    test: bool = False,\n    **kws: dict\n) → list\n```\n\nSegment the image to the single cells. \n\n\n\n**Args:**\n \n - \u003cb\u003e`imsegp`\u003c/b\u003e (str):  _description_ \n - \u003cb\u003e`fiterby_border_thickness`\u003c/b\u003e (int, optional):  _description_. Defaults to 100. \n - \u003cb\u003e`magnification`\u003c/b\u003e (int, optional):  _description_. Defaults to 100. \n - \u003cb\u003e`plotp`\u003c/b\u003e (str, optional):  _description_. Defaults to None. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  _description_ \n\n\n\n**Examples:**\n 1. Parameters:  prop_type='area',mn=100,mx=8000  at 1.5X  prop_type='area',mn=1500,mx=12000 \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/segment/region.py#L71\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_cellboxes`\n\n```python\nget_cellboxes(\n    regions: list,\n    cellbox_width: int = 150,\n    test: bool = False\n) → list\n```\n\nGet the bounding boxes of the cells. \n\n\n\n**Args:**\n \n - \u003cb\u003e`regions`\u003c/b\u003e (list):  regions. \n - \u003cb\u003e`cellbox_width`\u003c/b\u003e (int, optional):  width of the bounding box of the cell. Defaults to 150. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test-mode. Defaults to False. \n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  list of the bounding boxes for cells.  \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/segment/region.py#L109\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `arr_list2regions`\n\n```python\narr_list2regions(arr_list: list, time_increment: int) → tuple\n```\n\nParameterized cell-segmentation for the time lapse images.  \n\n\n\n**Args:**\n \n - \u003cb\u003e`arr_list`\u003c/b\u003e (list):  frames of images. \n - \u003cb\u003e`time_increment`\u003c/b\u003e (int):  time interval. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`tuple`\u003c/b\u003e:  regions and table with intensities. \n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.spt.io`\nI/O \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/io.py#L10\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `to_frames`\n\n```python\nto_frames(input_path: str, channeli=None)\n```\n\nConvert to frames. \n\n\n\n**Args:**\n \n - \u003cb\u003e`input_path`\u003c/b\u003e (str):  path to the raw data. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`list`\u003c/b\u003e:  list of frames. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/io.py#L41\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `expt_dh2expt_info`\n\n```python\nexpt_dh2expt_info(expt_dh: str) → DataFrame\n```\n\nMake configuration using the directory structure for an experiment. \n\n\n\n**Args:**\n \n - \u003cb\u003e`expt_dh`\u003c/b\u003e (str):  str \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/io.py#L78\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `createinfo`\n\n```python\ncreateinfo(expt_dh: str) → str\n```\n\nCreate information file. \n\n\n\n**Args:**\n \n - \u003cb\u003e`expt_dh`\u003c/b\u003e (str):  path to the directory containing the raw data. \n\n\n\n**Returns:**\n path to the file containing the metadata.  \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.spt`\n\n\n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.spt.stat`\nStatistical analysis of the single particle tracking. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L22\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `test_locate_particles`\n\n```python\ntest_locate_particles(\n    cellcfg: dict,\n    params_locate: dict,\n    frame=None,\n    force: bool = False,\n    test: bool = False\n) → bool\n```\n\nTest locating of the particles. \n\n\n\n**Args:**\n \n - \u003cb\u003e`cellcfg`\u003c/b\u003e (dict):  the cell level configuration.  \n - \u003cb\u003e`params_locate`\u003c/b\u003e (dict):  parameters provided for the location. \n - \u003cb\u003e`frame`\u003c/b\u003e (np.array, optional):  image frame. Defaults to None. \n - \u003cb\u003e`force`\u003c/b\u003e (bool, optional):  over-write the outputs. Defaults to False. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test mode. Defaults to False. \n\n\n\n**Returns:**\n bool \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L89\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `to_msd`\n\n```python\nto_msd(\n    frames: list,\n    coff_intesity_perc: float = 75,\n    diameter=11,\n    cores: int = 4,\n    test: bool = False\n) → tuple\n```\n\nMSD from the nd file. \n\n\n\n**Args:**\n \n - \u003cb\u003e`frames`\u003c/b\u003e (str):  2D frames. \n\n\n\n\n\n**Returns:**\n \n - \u003cb\u003e`tuple`\u003c/b\u003e:  outputs. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L126\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `trim_returns`\n\n```python\ntrim_returns(df1: DataFrame) → DataFrame\n```\n\nTrim images. \n\n\n\n**Args:**\n \n - \u003cb\u003e`df1`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L175\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `fill_frame_jumps`\n\n```python\nfill_frame_jumps(df1: DataFrame, jump_length) → DataFrame\n```\n\nFill the frame jumps. \n\n\n\n**Args:**\n \n - \u003cb\u003e`df1`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n - \u003cb\u003e`jump_length`\u003c/b\u003e (_type_):  length of the jump. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L202\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `cellcfg2distances`\n\n```python\ncellcfg2distances(\n    cellcfg: dict,\n    params: dict,\n    subtract_drift: bool = False,\n    test: bool = False,\n    force: bool = False\n)\n```\n\nCalculate distances from cell configuration. \n\n\n\n**Args:**\n \n - \u003cb\u003e`cellcfg`\u003c/b\u003e (dict):  configuration \n - \u003cb\u003e`params`\u003c/b\u003e (_type_, optional):  parameters. Defaults to { 'locate':{'diameter':11, # round to odd number 'noise_size':1, 'separation':15, 'threshold':4000, 'preprocess':True, 'invert':False, 'max_iterations':50, 'percentile':0, 'engine':'numba', }, 'link_df':{ 'search_range':5, 'memory':1, 'link_strategy':'drop',}, 'filter_stubs':{'threshold':4}, 'get_distance_from_centroid':{'center':[75,75]}, }. \n - \u003cb\u003e`force`\u003c/b\u003e (bool, optional):  over-write the outputs. Defaults to False. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L308\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `apply_cellcfgp2distances`\n\n```python\napply_cellcfgp2distances(cellcfgp: str)\n```\n\nWrapper around cellcfg2distances for multiprocessing. \n\n\n\n**Args:**\n \n - \u003cb\u003e`cellcfgp`\u003c/b\u003e (str):  path to the configuration file. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L325\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_distance_from_centroid`\n\n```python\nget_distance_from_centroid(df1: DataFrame, center: list = [75, 75]) → DataFrame\n```\n\nGet distance from the centroid. \n\n\n\n**Args:**\n \n - \u003cb\u003e`df1`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n - \u003cb\u003e`center`\u003c/b\u003e (list, optional):  center point. Defaults to [75,75]. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L352\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `distance_effective`\n\n```python\ndistance_effective(particle, frame1, frame2, t_cor: DataFrame) → float\n```\n\nEffective distance between frames. \n\n\n\n**Args:**\n \n - \u003cb\u003e`particle `\u003c/b\u003e:  particle \n - \u003cb\u003e`frame1`\u003c/b\u003e (np.array):  a frame. \n - \u003cb\u003e`frame2`\u003c/b\u003e (np.array):  another frame. \n - \u003cb\u003e`t_cor`\u003c/b\u003e (pd.DataFrame):  t_cor. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`float`\u003c/b\u003e:  distance \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/spt/stat.py#L375\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `get_distance_travelled`\n\n```python\nget_distance_travelled(t_cor: DataFrame) → DataFrame\n```\n\nDistance travelled. \n\n\n\n**Args:**\n \n - \u003cb\u003e`t_cor`\u003c/b\u003e (pd.DataFrame):  input dataframe. \n\n\n\n**Returns:**\n \n - \u003cb\u003e`pd.DataFrame`\u003c/b\u003e:  output dataframe. \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.viz.colors`\nGLobally used variables. \n\n**Global Variables**\n---------------\n- **r**\n- **g**\n- **b**\n- **cmap_gfp_list**\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.viz.image`\nVisualization of the images. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz/image.py#L7\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `image_background`\n\n```python\nimage_background(\n    img_region=None,\n    img=None,\n    cmap: str = 'binary_r',\n    alpha=1,\n    linewidths=1,\n    colors='cyan',\n    kws_region={},\n    show_scalebar=None,\n    scalebar_color: str = 'w',\n    show_cbar: bool = True,\n    test=False,\n    ax=None,\n    **kws_img\n) → Axes\n```\n\nPlot the image, to be used as a background to the annotations. \n\n\n\n**Args:**\n \n - \u003cb\u003e`img_region`\u003c/b\u003e (_type_, optional):  segmentation image. Defaults to None. \n - \u003cb\u003e`img`\u003c/b\u003e (_type_, optional):  image with intensity values. Defaults to None. \n - \u003cb\u003e`cmap`\u003c/b\u003e (str, optional):  colormap name. Defaults to 'binary_r'. \n - \u003cb\u003e`alpha`\u003c/b\u003e (int, optional):  transparency. Defaults to 1. \n - \u003cb\u003e`linewidths`\u003c/b\u003e (int, optional):  segmentation contour line width. Defaults to 1. \n - \u003cb\u003e`colors`\u003c/b\u003e (str, optional):  color of the segmentation line. Defaults to 'cyan'. \n - \u003cb\u003e`kws_region`\u003c/b\u003e (dict, optional):  parameters provided to the segmentation plot. Defaults to {}. \n - \u003cb\u003e`show_scalebar`\u003c/b\u003e (_type_, optional):  show scale bar. Defaults to None. \n - \u003cb\u003e`scalebar_color`\u003c/b\u003e (str, optional):  color of the scale bar. Defaults to 'w'. \n - \u003cb\u003e`show_cbar`\u003c/b\u003e (bool, optional):  show colorbar. Defaults to True. \n - \u003cb\u003e`test`\u003c/b\u003e (bool, optional):  test-mode. Defaults to False. \n - \u003cb\u003e`ax`\u003c/b\u003e (_type_, optional):  subplot object. Defaults to None. \n\nKeyword Args: parameters provided to the `plt.imshow`. \n\n**Returns:**\n plt.Axes \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz/image.py#L87\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `annot_cells`\n\n```python\nannot_cells(label_image, show_boxes: bool = False, ax: Axes = None) → Axes\n```\n\nAnnotate the cells on an image. \n\n\n\n**Args:**\n \n - \u003cb\u003e`label_image`\u003c/b\u003e (_type_):  image with the labeled regions  \n - \u003cb\u003e`show_boxes`\u003c/b\u003e (bool, optional):  show boxes around regions. Defaults to False. \n - \u003cb\u003e`ax`\u003c/b\u003e (plt.Axes, optional):  plt.Axes. Defaults to None. \n\n\n\n**Returns:**\n plt.Axes \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz/image.py#L114\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `image_regions_annotated`\n\n```python\nimage_regions_annotated(\n    img_region,\n    img,\n    show_boxes: bool = False,\n    **kws_img\n) → Axes\n```\n\nImage with the annotated regions. Usage: for QC of the segmentation. \n\n\n\n**Args:**\n \n - \u003cb\u003e`img_region`\u003c/b\u003e (_type_):  image with segmentated regions. \n - \u003cb\u003e`img`\u003c/b\u003e (_type_):  image with intensity. \n - \u003cb\u003e`show_boxes`\u003c/b\u003e (bool, optional):  whether to show the boxes around the regions. Defaults to False. \n\nKeyword Args: parameters provided to the `image_background` function. \n\n\n\n**Returns:**\n plt.Axes \n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.viz`\n\n\n\n\n\n\n\u003c!-- markdownlint-disable --\u003e\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz.py#L0\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n## \u003ckbd\u003emodule\u003c/kbd\u003e `htsimaging.viz.stat`\nVisualization of the statistics. \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz/stat.py#L6\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `dist_signal`\n\n```python\ndist_signal(\n    img,\n    threshold: float = None,\n    label_threshold: float = None,\n    params_axvline: dict = {'color': 'r', 'linestyle': 'dashed'},\n    ax: Axes = None,\n    **kws\n) → Axes\n```\n\nPlot the distribution of intensity. \n\n\n\n**Args:**\n \n - \u003cb\u003e`img`\u003c/b\u003e (_type_):  inpput image \n - \u003cb\u003e`threshold`\u003c/b\u003e (float, optional):  threshold applied. Defaults to None. \n - \u003cb\u003e`label_threshold`\u003c/b\u003e (float, optional):  label of the threshold. Defaults to None. \n - \u003cb\u003e`params_axvline`\u003c/b\u003e (_type_, optional):  parameters provided to the vertical line plot. Defaults to {'color':'r','linestyle':'dashed'}. \n - \u003cb\u003e`ax`\u003c/b\u003e (plt.Axes, optional):  subplot object. Defaults to None. \n\nKeyword Args: parameters provided to the `hist` function.  \n\n\n\n**Returns:**\n plt.Axes \n\n\n---\n\n\u003ca href=\"https://github.com/rraadd88/htsimaging/blob/master/htsimaging/viz/stat.py#L42\"\u003e\u003cimg align=\"right\" style=\"float:right;\" src=\"https://img.shields.io/badge/-source-cccccc?style=flat-square\"\u003e\u003c/a\u003e\n\n### \u003ckbd\u003efunction\u003c/kbd\u003e `plot_summary_stats`\n\n```python\nplot_summary_stats(input_paths: list, ax: Axes = None) → Axes\n```\n\nPlot summary stats for a set of images e.g. time-lapse images. \n\n\n\n**Args:**\n \n - \u003cb\u003e`input_paths`\u003c/b\u003e (list):  list of paths of the images. \n - \u003cb\u003e`ax`\u003c/b\u003e (plt.Axes, optional):  subplot object. Defaults to None. \n\n\n\n**Returns:**\n plt.Axes \n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frraadd88%2Fhtsimaging","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frraadd88%2Fhtsimaging","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frraadd88%2Fhtsimaging/lists"}