Note
Go to the end to download the full example code.
Animate 3D#
Display a labels layer above of an image layer using the add_labels and add_image APIs
Rendering frames...
0%| | 0/151 [00:00<?, ?it/s]IMAGEIO FFMPEG_WRITER WARNING: input image is not divisible by macro_block_size=16, resizing from (1086, 635) to (1088, 640) 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%| | 1/151 [00:00<00:53, 2.79it/s]
1%|▏ | 2/151 [00:00<00:51, 2.89it/s]
2%|▏ | 3/151 [00:00<00:47, 3.14it/s]
3%|▎ | 4/151 [00:01<00:44, 3.34it/s]
3%|▎ | 5/151 [00:01<00:42, 3.47it/s]
4%|▍ | 6/151 [00:01<00:39, 3.64it/s]
5%|▍ | 7/151 [00:02<00:37, 3.79it/s]
5%|▌ | 8/151 [00:02<00:36, 3.94it/s]
6%|▌ | 9/151 [00:02<00:34, 4.12it/s]
7%|▋ | 10/151 [00:02<00:32, 4.31it/s]
7%|▋ | 11/151 [00:02<00:31, 4.51it/s]
8%|▊ | 12/151 [00:03<00:29, 4.69it/s]
9%|▊ | 13/151 [00:03<00:28, 4.92it/s]
9%|▉ | 14/151 [00:03<00:26, 5.13it/s]
10%|▉ | 15/151 [00:03<00:25, 5.39it/s]
11%|█ | 16/151 [00:03<00:24, 5.52it/s]
11%|█▏ | 17/151 [00:03<00:23, 5.69it/s]
12%|█▏ | 18/151 [00:04<00:23, 5.71it/s]
13%|█▎ | 19/151 [00:04<00:23, 5.70it/s]
13%|█▎ | 20/151 [00:04<00:22, 5.72it/s]
14%|█▍ | 21/151 [00:04<00:21, 5.93it/s]
15%|█▍ | 22/151 [00:04<00:21, 5.99it/s]
15%|█▌ | 23/151 [00:04<00:21, 5.95it/s]
16%|█▌ | 24/151 [00:05<00:20, 6.10it/s]
17%|█▋ | 25/151 [00:05<00:20, 6.19it/s]
17%|█▋ | 26/151 [00:05<00:20, 6.06it/s]
18%|█▊ | 27/151 [00:05<00:20, 6.04it/s]
19%|█▊ | 28/151 [00:05<00:20, 5.95it/s]
19%|█▉ | 29/151 [00:05<00:20, 5.96it/s]
20%|█▉ | 30/151 [00:06<00:20, 6.02it/s]
21%|██ | 31/151 [00:06<00:19, 6.03it/s]
21%|██ | 32/151 [00:06<00:19, 6.03it/s]
22%|██▏ | 33/151 [00:06<00:19, 6.09it/s]
23%|██▎ | 34/151 [00:06<00:19, 6.02it/s]
23%|██▎ | 35/151 [00:06<00:19, 6.07it/s]
24%|██▍ | 36/151 [00:07<00:18, 6.06it/s]
25%|██▍ | 37/151 [00:07<00:18, 6.05it/s]
25%|██▌ | 38/151 [00:07<00:18, 6.01it/s]
26%|██▌ | 39/151 [00:07<00:18, 5.96it/s]
26%|██▋ | 40/151 [00:07<00:18, 5.96it/s]
27%|██▋ | 41/151 [00:07<00:18, 5.98it/s]
28%|██▊ | 42/151 [00:08<00:18, 5.98it/s]
28%|██▊ | 43/151 [00:08<00:19, 5.67it/s]
29%|██▉ | 44/151 [00:08<00:19, 5.63it/s]
30%|██▉ | 45/151 [00:08<00:18, 5.62it/s]
30%|███ | 46/151 [00:08<00:18, 5.69it/s]
31%|███ | 47/151 [00:08<00:18, 5.75it/s]
32%|███▏ | 48/151 [00:09<00:17, 5.80it/s]
32%|███▏ | 49/151 [00:09<00:17, 5.84it/s]
33%|███▎ | 50/151 [00:09<00:17, 5.79it/s]
34%|███▍ | 51/151 [00:09<00:17, 5.87it/s]
34%|███▍ | 52/151 [00:09<00:16, 5.85it/s]
35%|███▌ | 53/151 [00:09<00:16, 5.93it/s]
36%|███▌ | 54/151 [00:10<00:17, 5.68it/s]
36%|███▋ | 55/151 [00:10<00:16, 5.84it/s]
37%|███▋ | 56/151 [00:10<00:16, 5.86it/s]
38%|███▊ | 57/151 [00:10<00:16, 5.73it/s]
38%|███▊ | 58/151 [00:10<00:15, 5.87it/s]
39%|███▉ | 59/151 [00:11<00:15, 5.84it/s]
40%|███▉ | 60/151 [00:11<00:15, 5.77it/s]
40%|████ | 61/151 [00:11<00:15, 5.78it/s]
41%|████ | 62/151 [00:11<00:15, 5.74it/s]
42%|████▏ | 63/151 [00:11<00:15, 5.64it/s]
42%|████▏ | 64/151 [00:11<00:15, 5.58it/s]
43%|████▎ | 65/151 [00:12<00:15, 5.58it/s]
44%|████▎ | 66/151 [00:12<00:14, 5.69it/s]
44%|████▍ | 67/151 [00:12<00:15, 5.58it/s]
45%|████▌ | 68/151 [00:12<00:14, 5.73it/s]
46%|████▌ | 69/151 [00:12<00:14, 5.70it/s]
46%|████▋ | 70/151 [00:12<00:13, 5.79it/s]
47%|████▋ | 71/151 [00:13<00:13, 5.87it/s]
48%|████▊ | 72/151 [00:13<00:13, 5.71it/s]
48%|████▊ | 73/151 [00:13<00:13, 5.61it/s]
49%|████▉ | 74/151 [00:13<00:13, 5.69it/s]
50%|████▉ | 75/151 [00:13<00:13, 5.56it/s]
50%|█████ | 76/151 [00:14<00:13, 5.66it/s]
51%|█████ | 77/151 [00:14<00:13, 5.58it/s]
52%|█████▏ | 78/151 [00:14<00:13, 5.60it/s]
52%|█████▏ | 79/151 [00:14<00:12, 5.56it/s]
53%|█████▎ | 80/151 [00:14<00:12, 5.65it/s]
54%|█████▎ | 81/151 [00:14<00:12, 5.68it/s]
54%|█████▍ | 82/151 [00:15<00:12, 5.60it/s]
55%|█████▍ | 83/151 [00:15<00:12, 5.62it/s]
56%|█████▌ | 84/151 [00:15<00:11, 5.61it/s]
56%|█████▋ | 85/151 [00:15<00:12, 5.49it/s]
57%|█████▋ | 86/151 [00:15<00:11, 5.61it/s]
58%|█████▊ | 87/151 [00:15<00:11, 5.72it/s]
58%|█████▊ | 88/151 [00:16<00:10, 5.83it/s]
59%|█████▉ | 89/151 [00:16<00:10, 5.68it/s]
60%|█████▉ | 90/151 [00:16<00:10, 5.78it/s]
60%|██████ | 91/151 [00:16<00:10, 5.66it/s]
61%|██████ | 92/151 [00:16<00:10, 5.74it/s]
62%|██████▏ | 93/151 [00:17<00:10, 5.74it/s]
62%|██████▏ | 94/151 [00:17<00:09, 5.72it/s]
63%|██████▎ | 95/151 [00:17<00:09, 5.85it/s]
64%|██████▎ | 96/151 [00:17<00:09, 5.94it/s]
64%|██████▍ | 97/151 [00:17<00:09, 5.88it/s]
65%|██████▍ | 98/151 [00:17<00:09, 5.70it/s]
66%|██████▌ | 99/151 [00:18<00:09, 5.73it/s]
66%|██████▌ | 100/151 [00:18<00:08, 5.70it/s]
67%|██████▋ | 101/151 [00:18<00:08, 5.79it/s]
68%|██████▊ | 102/151 [00:18<00:08, 5.88it/s]
68%|██████▊ | 103/151 [00:18<00:08, 5.99it/s]
69%|██████▉ | 104/151 [00:18<00:07, 6.03it/s]
70%|██████▉ | 105/151 [00:19<00:07, 5.95it/s]
70%|███████ | 106/151 [00:19<00:07, 6.04it/s]
71%|███████ | 107/151 [00:19<00:07, 6.15it/s]
72%|███████▏ | 108/151 [00:19<00:06, 6.22it/s]
72%|███████▏ | 109/151 [00:19<00:06, 6.07it/s]
73%|███████▎ | 110/151 [00:19<00:06, 5.98it/s]
74%|███████▎ | 111/151 [00:20<00:06, 5.98it/s]
74%|███████▍ | 112/151 [00:20<00:06, 6.03it/s]
75%|███████▍ | 113/151 [00:20<00:06, 6.14it/s]
75%|███████▌ | 114/151 [00:20<00:05, 6.20it/s]
76%|███████▌ | 115/151 [00:20<00:05, 6.18it/s]
77%|███████▋ | 116/151 [00:20<00:05, 6.20it/s]
77%|███████▋ | 117/151 [00:21<00:05, 6.12it/s]
78%|███████▊ | 118/151 [00:21<00:05, 6.04it/s]
79%|███████▉ | 119/151 [00:21<00:05, 6.14it/s]
79%|███████▉ | 120/151 [00:21<00:05, 6.18it/s]
80%|████████ | 121/151 [00:21<00:04, 6.11it/s]
81%|████████ | 122/151 [00:21<00:04, 6.15it/s]
81%|████████▏ | 123/151 [00:22<00:04, 5.88it/s]
82%|████████▏ | 124/151 [00:22<00:04, 5.84it/s]
83%|████████▎ | 125/151 [00:22<00:04, 5.75it/s]
83%|████████▎ | 126/151 [00:22<00:04, 5.72it/s]
84%|████████▍ | 127/151 [00:22<00:04, 5.84it/s]
85%|████████▍ | 128/151 [00:22<00:03, 5.88it/s]
85%|████████▌ | 129/151 [00:23<00:03, 5.72it/s]
86%|████████▌ | 130/151 [00:23<00:03, 5.67it/s]
87%|████████▋ | 131/151 [00:23<00:03, 5.63it/s]
87%|████████▋ | 132/151 [00:23<00:03, 5.79it/s]
88%|████████▊ | 133/151 [00:23<00:03, 5.78it/s]
89%|████████▊ | 134/151 [00:23<00:02, 5.71it/s]
89%|████████▉ | 135/151 [00:24<00:02, 5.78it/s]
90%|█████████ | 136/151 [00:24<00:02, 5.88it/s]
91%|█████████ | 137/151 [00:24<00:02, 5.72it/s]
91%|█████████▏| 138/151 [00:24<00:02, 5.65it/s]
92%|█████████▏| 139/151 [00:24<00:02, 5.46it/s]
93%|█████████▎| 140/151 [00:25<00:02, 5.33it/s]
93%|█████████▎| 141/151 [00:25<00:01, 5.23it/s]
94%|█████████▍| 142/151 [00:25<00:01, 5.03it/s]
95%|█████████▍| 143/151 [00:25<00:01, 4.81it/s]
95%|█████████▌| 144/151 [00:25<00:01, 4.56it/s]
96%|█████████▌| 145/151 [00:26<00:01, 4.18it/s]
97%|█████████▋| 146/151 [00:26<00:01, 3.89it/s]
97%|█████████▋| 147/151 [00:26<00:01, 3.72it/s]
98%|█████████▊| 148/151 [00:27<00:00, 3.64it/s]
99%|█████████▊| 149/151 [00:27<00:00, 3.55it/s]
99%|█████████▉| 150/151 [00:27<00:00, 3.44it/s]
100%|██████████| 151/151 [00:28<00:00, 3.33it/s]
100%|██████████| 151/151 [00:28<00:00, 5.39it/s]
from skimage import data
from scipy import ndimage as ndi
from napari_animation import Animation
import napari
blobs = data.binary_blobs(length=128, volume_fraction=0.1, n_dim=3)
viewer = napari.view_image(blobs.astype(float), name="blobs")
labeled = ndi.label(blobs)[0]
viewer.add_labels(labeled, name="blob ID")
animation = Animation(viewer)
viewer.update_console({"animation": animation})
viewer.dims.ndisplay = 3
viewer.camera.angles = (0.0, 0.0, 90.0)
animation.capture_keyframe()
viewer.camera.zoom = 2.4
animation.capture_keyframe()
viewer.camera.angles = (-7.0, 15.7, 62.4)
animation.capture_keyframe(steps=60)
viewer.camera.angles = (2.0, -24.4, -36.7)
animation.capture_keyframe(steps=60)
viewer.reset_view()
viewer.camera.angles = (0.0, 0.0, 90.0)
animation.capture_keyframe()
animation.animate("animate3D.mp4", canvas_only=False)
Total running time of the script: (0 minutes 32.282 seconds)