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At frame 0:
- change all channels' front clipping to 0

At frame 0:
- rotate by 20 degrees around (0, 0, 1)

From frame 0 to frame 400:
- rotate by 360 degrees horizontally
- rotate by 60 degrees vertically
- change all channels' front clipping to 200


From frame 400 to frame 600:
- change all channels' front clipping to 600

Simultaneous rotation around multiple axes. 3D animation of mouse colon tumors using blood vessel staining (CD31; red), ECi-based tissue clearing and a LaVision BioTec lightsheet UltraMicroscope II (see also Figure 1). The image volume is rotated around its y-axis (with a higher speed) and around the x-axis of the view (with a lower speed). Only a couple of text lines are required to describe an animation which is hard to achieve with key frame-based animation.

At frame 0:
- change channel 1 intensity to (130.0, 2000.0, 0.2)
- change channel 1 alpha to (130.0, 2000.0, 0.2)
- change channel 1 color to (255.0, 255.0, 255.0)
- change channel 1 weight to 1.0
- change all channels' front/back clipping to (-5000, 5000)
- change rendering algorithm to maximum intensity 
- change timepoint to 0
- reset transformation
- zoom by a factor of 0.8


From frame 0 to frame 560 change timepoint to 480
From frame 200 to frame 520 rotate by -360 degrees vertically 
From frame 200 to frame 560 zoom by a factor of 1.8 ease-in

Animated transformation through time. Animation of a growing zebrafish nervous system, imaged on a custom built lightsheet microscope. While the time-lapse progresses, the image volume is spatially transformed. Scale bar 100 µm

At frame 0:
- zoom by a factor of 0.6
- rotate by 180 degrees around (0, 0, 1)
- change all channels' front clipping to -1000

From frame 20 to frame 260 rotate by sin degrees horizontally 

From frame 0 to frame 260 zoom by a factor of 2 ease-out 
From frame 0 to frame 20 rotate by -60 degrees vertically ease-out

From frame 80 to frame 90:
- change channel 2 weight to 0
- change channel 3 weight to 0

From frame 140 to frame 150:
- change channel 1 weight to 0
- change channel 2 weight to 1

From frame 200 to frame 210:
- change channel 2 weight to 0
- change channel 3 weight to 1

From frame 260 to frame 270:
- change channel 1 weight to 1
- change channel 2 weight to 1

script
function sin(t) {
    return 180 * abs(sin(2 * PI * (t-80) / 120));
}

Simultaneous pivoting and channel switching. Animation of a mouse paw, imaged on a LaVision BioTec lightsheet UltraMicroscope II. Pivoting is implemented using a macro.

At frame 0:
- reset transformation 
- change all channels' front clipping to -1000

// first position
From frame 0 to frame 40:
- zoom by a factor of 3.4
- translate by (-806.5, -159.2, 0.0)

At frame 40:
- change all channels' front clipping to -130
From frame 40 to frame 80:
- change all channels' front clipping to 100
From frame 80 to frame 120:
- change all channels' front clipping to -130
At frame 120:
- change all channels' front clipping to -1000

From frame 120 to frame 160:
- zoom by a factor of 0.3
- translate by (234.5, 46.3, 0.0)


// second position
From frame 160 to frame 200:
- zoom by a factor of 3.6
- translate by (888.6, -1082.0, -0.0)

At frame 200:
- change all channels' front clipping to -130
From frame 200 to frame 240:
- change all channels' front clipping to 0
From frame 240 to frame 280:
- change all channels' front clipping to -130
At frame 280:
- change all channels' front clipping to -1000

From frame 280 to frame 320:
- zoom by a factor of 0.3
- translate by (-235.8, 297.5, -0.0)


// third position
From frame 320 to frame 360:
- zoom by a factor of 3.0
- translate by (-454.4, 2248.4, -0.0)

At frame 360:
- change all channels' front clipping to -80
From frame 360 to frame 400:
- change all channels' front clipping to 80
From frame 400 to frame 440:
- change all channels' front clipping to -80
At frame 440:
- change all channels' front clipping to -1000

From frame 440 to frame 480:
- zoom by a factor of 0.3
- translate by (117.0, -655.3, -0.0)

Consecutive zoom-in and scroll-through at different positions. Animation of a mouse paw, imaged on a LaVision BioTec lightsheet UltraMicroscope II.

From frame 90 to frame 450:
- rotate by 360 degrees around (0, 0, 1)

At frame 0:
- rotate by 10 degrees vertically
- rotate by 10 degrees horizontally
- change all channels' front clipping to -5000
- change all channels' bounding box max z to 500

From frame 0 to frame 90:
- rotate by 180 degrees vertically
- zoom by a factor of zoomf


From frame 90 to frame 450:
- change all channels' bounding box max z to 0

script
function zoomf(t) {
    return 0.6 - 0.3 * abs(sin(2 * PI * t / 180));
}

Macro for parameterized zooming. Animation of a human cornea, imaged on a Zeiss LSM880 NLO 2-photon microscope. The data set is elongated in one dimension. Instead of zooming out during the entire animation, the zoom is adjusted to the rotation to always fill the available movie canvas optimally, using a macro.

From frame 0 to frame 100:
- rotate by -360 degrees horizontally
- translate horizontally by tr
- zoom by a factor of z

From frame 80 to frame 120 translate by (0, 0, 80) ease-in-out
From frame 120 to frame 190 translate by (0, 0, -160) ease-in-out
From frame 190 to frame 230 translate by (0, 0, 80) ease-in-out

script
function z(t) {
    return 0.75 + 0.25 * cos(2 * PI * t / 100);
}

script
function tr(t) {
    return 128 * cos(2 * PI * (t+25) / 100);
}

Rendering of an MRI image volume of a human head using the BigDataViewer. To demonstrate the extendibility of our framework, we wrote an adapter for Fiji’s BigDataViewer.

At frame 0 change lens to (1.4, 1, -3)
From frame 170 to frame 190 change lens to (0.6, 1.8, 0) ease-out
From frame 340 to frame 360 change lens to (1.4, 1, -3) ease-out

From frame 0 to frame 360 rotate by rot degrees horizontally


script
function rot(t) {
    return 30 * sin(2 * PI * t / 120);
}

Rendering of an organoid from the mouse intestine in an artificial laboratory environment. To demonstrate extendibility of our framework, we wrote an adapter that uses POV-Ray, a software for photorealistic rendering, instead of the integrated 3D renderer.

Composing an animation. This screencast demonstrates how the animation of the human cornea is built up and highlights the auto-completion features of the Animation Editor. A detailed step-by-step description is also found in the manual.

A dedicated animation editor, based on Fiji's script editor, facilitates the composition of the animation description with auto-completion and recording capabilities.

The dedicated animation editor can record different rendering states and automatically create the description text to transition between them.

3Dscript

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