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 (959, 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).

  1%|          | 1/121 [00:00<00:12,  9.53it/s]
  3%|▎         | 4/121 [00:00<00:05, 21.22it/s]
  7%|▋         | 8/121 [00:00<00:04, 27.47it/s]
 10%|▉         | 12/121 [00:00<00:03, 30.30it/s]
 13%|█▎        | 16/121 [00:00<00:03, 31.73it/s]
 17%|█▋        | 20/121 [00:00<00:03, 32.72it/s]
 20%|█▉        | 24/121 [00:00<00:02, 33.50it/s]
 23%|██▎       | 28/121 [00:00<00:02, 34.10it/s]
 26%|██▋       | 32/121 [00:01<00:02, 34.80it/s]
 30%|██▉       | 36/121 [00:01<00:02, 35.02it/s]
 33%|███▎      | 40/121 [00:01<00:02, 35.16it/s]
 36%|███▋      | 44/121 [00:01<00:02, 34.51it/s]
 40%|███▉      | 48/121 [00:01<00:02, 33.20it/s]
 43%|████▎     | 52/121 [00:01<00:02, 33.18it/s]
 46%|████▋     | 56/121 [00:01<00:01, 33.26it/s]
 50%|████▉     | 60/121 [00:01<00:01, 33.31it/s]
 53%|█████▎    | 64/121 [00:02<00:03, 16.81it/s]
 55%|█████▌    | 67/121 [00:02<00:03, 13.81it/s]
 58%|█████▊    | 70/121 [00:03<00:04, 12.16it/s]
 60%|█████▉    | 72/121 [00:03<00:04, 11.35it/s]
 61%|██████    | 74/121 [00:03<00:04, 10.88it/s]
 63%|██████▎   | 76/121 [00:03<00:04, 10.52it/s]
 64%|██████▍   | 78/121 [00:03<00:04, 10.41it/s]
 66%|██████▌   | 80/121 [00:04<00:03, 10.35it/s]
 68%|██████▊   | 82/121 [00:04<00:03, 10.48it/s]
 69%|██████▉   | 84/121 [00:04<00:03, 10.53it/s]
 71%|███████   | 86/121 [00:04<00:03, 10.68it/s]
 73%|███████▎  | 88/121 [00:04<00:03, 10.69it/s]
 74%|███████▍  | 90/121 [00:04<00:02, 10.73it/s]
 76%|███████▌  | 92/121 [00:05<00:03,  8.31it/s]
 78%|███████▊  | 94/121 [00:05<00:03,  8.94it/s]
 79%|███████▉  | 96/121 [00:05<00:02,  9.38it/s]
 81%|████████  | 98/121 [00:05<00:02,  9.77it/s]
 83%|████████▎ | 100/121 [00:06<00:02,  9.91it/s]
 84%|████████▍ | 102/121 [00:06<00:01, 10.04it/s]
 86%|████████▌ | 104/121 [00:06<00:01,  9.97it/s]
 88%|████████▊ | 106/121 [00:06<00:01,  9.89it/s]
 89%|████████▉ | 108/121 [00:06<00:01,  9.63it/s]
 90%|█████████ | 109/121 [00:07<00:01,  9.57it/s]
 91%|█████████ | 110/121 [00:07<00:01,  9.43it/s]
 92%|█████████▏| 111/121 [00:07<00:01,  9.26it/s]
 93%|█████████▎| 112/121 [00:07<00:01,  8.96it/s]
 93%|█████████▎| 113/121 [00:07<00:00,  8.95it/s]
 94%|█████████▍| 114/121 [00:07<00:00,  8.93it/s]
 95%|█████████▌| 115/121 [00:07<00:00,  8.85it/s]
 96%|█████████▌| 116/121 [00:07<00:00,  8.67it/s]
 97%|█████████▋| 117/121 [00:07<00:00,  8.69it/s]
 98%|█████████▊| 118/121 [00:08<00:00,  8.72it/s]
 98%|█████████▊| 119/121 [00:08<00:00,  8.77it/s]
 99%|█████████▉| 120/121 [00:08<00:00,  8.69it/s]
100%|██████████| 121/121 [00:08<00:00,  8.70it/s]
100%|██████████| 121/121 [00:08<00:00, 14.36it/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)