.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/plot_celegans.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_plot_celegans.py: Tracking the Undulating Motion of C. elegans ============================================ This example demonstrates how to track the characteristic undulating pattern of a moving C. elegans using splinebox. Data Source: `WormSwin `_ Data Used: csb-1_dataset 24_2_1_1 Preprocessing: * Background: Maximum projections of frames 75-187 (to account for minor movements). * Background Subtraction: Subtracted from each frame. * Cropping: Frames 141-187, focusing on a single worm centered at the bottom. * Image Adjustment: Rotation, contrast adjustment, and conversion to 8-bit. .. GENERATED FROM PYTHON SOURCE LINES 17-25 .. code-block:: Python import matplotlib.animation import matplotlib.pyplot as plt import numpy as np import skimage import splinebox .. GENERATED FROM PYTHON SOURCE LINES 27-29 Load the data and inspect it ---------------------------- .. GENERATED FROM PYTHON SOURCE LINES 29-44 .. code-block:: Python stack = skimage.io.imread("celegans.tif") def _update0(i): mpl_img.set_array(stack[i]) return (mpl_img,) fig, ax = plt.subplots(figsize=(7, 3)) mpl_img = ax.imshow(stack[0], cmap="Greys_r") ax.set(xlim=(0, stack.shape[2]), ylim=(0, stack.shape[1])) animation = matplotlib.animation.FuncAnimation(fig, _update0, len(stack), interval=100, blit=True) plt.show() .. container:: sphx-glr-animation .. raw:: html

.. GENERATED FROM PYTHON SOURCE LINES 45-48 Segmentation of the Worm ------------------------ Next, we segment the worm using Otsu's thresholding method to prepare for spline fitting. .. GENERATED FROM PYTHON SOURCE LINES 48-66 .. code-block:: Python thresh = skimage.filters.threshold_otsu(stack) mask = stack < thresh def _update1(i): mpl_img.set_array(stack[i]) mpl_mask.set_array(mask[i]) return (mpl_img, mpl_mask) fig, ax = plt.subplots(figsize=(7, 3)) mpl_img = ax.imshow(stack[0], cmap="Greys_r") mpl_mask = ax.imshow(mask[0], cmap="Reds", alpha=0.5) ax.set(xlim=(0, stack.shape[2]), ylim=(0, stack.shape[1])) animation = matplotlib.animation.FuncAnimation(fig, _update1, len(stack), interval=100, blit=True) plt.show() .. container:: sphx-glr-animation .. raw:: html

.. GENERATED FROM PYTHON SOURCE LINES 67-71 Fitting Splines to the Worm's Shape ----------------------------------- We fit a spline to the worm in each frame. The spline is created by skeletonizing the worm and then ordering the skeleton points based on their x-position. For simplicity, this method assumes that the worm is moving from left to right. In more complex scenarios, a graph-based approach (e.g., using the skan package) would be more appropriate for ordering the points. We use seven knots in our spline, balancing accuracy and robustness against segmentation imperfections. An exponential basis function is selected for the spline to enable the generation of trigonometric functions. .. GENERATED FROM PYTHON SOURCE LINES 71-107 .. code-block:: Python M = 7 basis_function = splinebox.basis_functions.Exponential(M) splines = [] for i in range(len(mask)): label_img = skimage.measure.label(mask[i]) label_biggest = np.argmax(np.bincount(label_img.flatten())[1:]) + 1 mask[i] = label_img == label_biggest mask[i] = skimage.morphology.binary_opening(mask[i]) mask[i] = skimage.morphology.remove_small_holes(mask[i], area_threshold=7) skeleton = skimage.morphology.skeletonize(mask[i]) spline = splinebox.spline_curves.Spline(M=M, basis_function=basis_function, closed=False) coords = np.stack(np.where(skeleton), axis=-1) coords = coords[np.argsort(coords[:, 1])] spline.fit(coords) splines.append(spline) t = np.linspace(0, M - 1, 500) def _update2(i): mpl_img.set_array(stack[i]) vals = splines[i].eval(t) mpl_line.set_data(vals[:, 1], vals[:, 0]) return (mpl_img, mpl_line) fig, ax = plt.subplots(figsize=(7, 3)) mpl_img = ax.imshow(stack[0], cmap="Greys_r") vals = splines[0].eval(t) (mpl_line,) = ax.plot(vals[:, 1], vals[:, 0]) ax.set(xlim=(0, stack.shape[2]), ylim=(0, stack.shape[1])) animation = matplotlib.animation.FuncAnimation(fig, _update2, len(stack), interval=100, blit=True) plt.show() .. container:: sphx-glr-animation .. raw:: html

.. GENERATED FROM PYTHON SOURCE LINES 108-111 Analyzing the Undulating Motion ------------------------------- To focus on the undulating motion, we translate the splines to their center of mass and rotate them to align horizontally. .. GENERATED FROM PYTHON SOURCE LINES 111-123 .. code-block:: Python for spline in splines: start_point = np.squeeze(spline.eval(0)) stop_point = np.squeeze(spline.eval(spline.M - 1)) angle = np.arctan2(*(stop_point - start_point)) c = np.cos(angle) s = np.sin(angle) rot_matrix = np.array([[c, -s], [s, c]]) spline.rotate(rot_matrix) com = np.mean(spline.eval(t), axis=0) spline.translate(-com) .. GENERATED FROM PYTHON SOURCE LINES 124-125 Finally, we visualize the isolated undulating movement and its associated curvature. .. GENERATED FROM PYTHON SOURCE LINES 125-154 .. code-block:: Python def _update3(i): vals = splines[i].eval(t) curvature = splines[i].curvature(t) normals = splines[i].normal(t) comb = vals + d * curvature[:, np.newaxis] * normals for p, mpl_tooth in zip(ps, mpl_teeth): mpl_tooth.set_data([[vals[p, 1], comb[p, 1]], [vals[p, 0], comb[p, 0]]]) mpl_curvature.set_data(comb[:, 1], comb[:, 0]) mpl_line.set_data(vals[:, 1], vals[:, 0]) return (*mpl_teeth, mpl_curvature, mpl_line) fig, ax = plt.subplots(figsize=(7, 3)) vals = splines[0].eval(t) curvature = splines[0].curvature(t) normals = splines[0].normal(t) d = 50 comb = vals + d * curvature[:, np.newaxis] * normals mpl_teeth = [] ps = np.arange(0, len(comb), 10) for p in ps: mpl_teeth.extend(ax.plot([vals[p, 1], comb[p, 1]], [vals[p, 0], comb[p, 0]], color="#568b22")) (mpl_curvature,) = ax.plot(comb[:, 1], comb[:, 0]) (mpl_line,) = ax.plot(vals[:, 1], vals[:, 0]) ax.set(xlim=(-60, 60), ylim=(-25, 25)) animation = matplotlib.animation.FuncAnimation(fig, _update3, len(stack), interval=100, blit=True) plt.show() .. container:: sphx-glr-animation .. raw:: html

.. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 33.313 seconds) .. _sphx_glr_download_auto_examples_plot_celegans.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_celegans.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_celegans.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_celegans.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_