Layer planes

Rendering frames...

  0%|          | 0/121 [00:00<?, ?it/s]IMAGEIO FFMPEG_WRITER WARNING: input image is not divisible by macro_block_size=16, resizing from (955, 941) to (960, 944) to ensure video compatibility with most codecs and players. To prevent resizing, make your input image divisible by the macro_block_size or set the macro_block_size to 1 (risking incompatibility).

  2%|▏         | 2/121 [00:00<00:08, 14.55it/s]
  5%|▍         | 6/121 [00:00<00:04, 25.08it/s]
  8%|▊         | 10/121 [00:00<00:03, 29.27it/s]
 12%|█▏        | 14/121 [00:00<00:03, 31.50it/s]
 15%|█▍        | 18/121 [00:00<00:03, 32.82it/s]
 18%|█▊        | 22/121 [00:00<00:02, 33.75it/s]
 21%|██▏       | 26/121 [00:00<00:02, 34.27it/s]
 25%|██▍       | 30/121 [00:00<00:02, 34.72it/s]
 28%|██▊       | 34/121 [00:01<00:02, 35.24it/s]
 31%|███▏      | 38/121 [00:01<00:02, 35.31it/s]
 35%|███▍      | 42/121 [00:01<00:02, 35.25it/s]
 38%|███▊      | 46/121 [00:01<00:02, 34.33it/s]
 41%|████▏     | 50/121 [00:01<00:02, 34.20it/s]
 45%|████▍     | 54/121 [00:01<00:01, 34.04it/s]
 48%|████▊     | 58/121 [00:01<00:01, 33.82it/s]
 51%|█████     | 62/121 [00:02<00:02, 23.16it/s]
 54%|█████▎    | 65/121 [00:02<00:02, 20.92it/s]
 56%|█████▌    | 68/121 [00:02<00:02, 19.53it/s]
 59%|█████▊    | 71/121 [00:02<00:02, 18.73it/s]
 61%|██████    | 74/121 [00:02<00:02, 18.04it/s]
 63%|██████▎   | 76/121 [00:02<00:02, 17.55it/s]
 64%|██████▍   | 78/121 [00:03<00:02, 17.40it/s]
 66%|██████▌   | 80/121 [00:03<00:02, 17.09it/s]
 68%|██████▊   | 82/121 [00:03<00:02, 17.06it/s]
 69%|██████▉   | 84/121 [00:03<00:02, 16.73it/s]
 71%|███████   | 86/121 [00:03<00:02, 16.59it/s]
 73%|███████▎  | 88/121 [00:03<00:02, 16.29it/s]
 74%|███████▍  | 90/121 [00:03<00:01, 16.44it/s]
 76%|███████▌  | 92/121 [00:04<00:02, 11.15it/s]
 78%|███████▊  | 94/121 [00:04<00:02, 12.25it/s]
 79%|███████▉  | 96/121 [00:04<00:01, 13.00it/s]
 81%|████████  | 98/121 [00:04<00:01, 13.75it/s]
 83%|████████▎ | 100/121 [00:04<00:01, 14.20it/s]
 84%|████████▍ | 102/121 [00:04<00:01, 14.71it/s]
 86%|████████▌ | 104/121 [00:04<00:01, 14.94it/s]
 88%|████████▊ | 106/121 [00:04<00:00, 15.24it/s]
 89%|████████▉ | 108/121 [00:05<00:00, 15.17it/s]
 91%|█████████ | 110/121 [00:05<00:00, 15.26it/s]
 93%|█████████▎| 112/121 [00:05<00:00, 15.10it/s]
 94%|█████████▍| 114/121 [00:05<00:00, 15.16it/s]
 96%|█████████▌| 116/121 [00:05<00:00, 15.22it/s]
 98%|█████████▊| 118/121 [00:05<00:00, 15.40it/s]
 99%|█████████▉| 120/121 [00:05<00:00, 15.21it/s]
100%|██████████| 121/121 [00:05<00:00, 20.31it/s]

from scipy import ndimage as ndi
from napari_animation import Animation
import napari
import skimage
import scipy

viewer = napari.Viewer(ndisplay=3)

nuclei = skimage.data.cells3d()[:,1,...]
denoised = scipy.ndimage.median_filter(nuclei, size=3)
th_nuclei = denoised > skimage.filters.threshold_li(denoised)
th_nuclei = skimage.morphology.remove_small_holes(th_nuclei, 20**3)
labels_data = skimage.measure.label(th_nuclei)

animation = Animation(viewer)

image_layer = viewer.add_image(nuclei, name="nuclei", depiction="plane",
                               blending='translucent')
labels_layer = viewer.add_labels(labels_data, name="labels", blending='translucent')

viewer.camera.angles = (-18.23797054423494, 41.97404742075617, 141.96173085742896)
viewer.camera.zoom *= 0.5


def replace_labels_data():
    z_cutoff = int(image_layer.plane.position[0])
    new_labels_data = labels_data.copy()
    new_labels_data[z_cutoff:] = 0
    labels_layer.data = new_labels_data


labels_layer.visible = False
image_layer.plane.position = (0, 0, 0)
animation.capture_keyframe(steps=30)

image_layer.plane.position = (59, 0, 0)
animation.capture_keyframe(steps=30)

image_layer.plane.position = (0, 0, 0)

animation.capture_keyframe(steps=30)

image_layer.plane.events.position.connect(replace_labels_data)
labels_layer.visible = True
labels_layer.experimental_clipping_planes = [{
    "position": (0, 0, 0),
    "normal": (-1, 0, 0),  # point up in z (i.e: show stuff above plane)
}]

image_layer.plane.position = (59, 0, 0)
# access first plane, since it's a list
labels_layer.experimental_clipping_planes[0].position = (59, 0, 0)
animation.capture_keyframe(steps=30)

image_layer.plane.position = (0, 0, 0)
animation.capture_keyframe(steps=30)

animation.animate("layer_planes.mp4", canvas_only=True)
image_layer.plane.position = (0, 0, 0)