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How turn Z stacks into animation

Confocal microscopes are designed to collect data in three dimensions ( four if you do time lapse ) but how often do we make full use of that in our presentations. Here's a simple way to show off when displaying a Z stack from a Zeiss microscope.

Zen makes life very easy with its export image sequence settings, you could also export an AVI but the files are huge and not always easy to handle in other packages.

First collect your data - I'm not going to go into that here but going for the 'Optimal' setting in Z stack control is a really good plan as it will ensure a smooth stack with minimal interpolation. My example data are pollen grains stained with propidium iodide because they're a good test of resolving power, they look good and I'm a bee keeper so not exactly short of pollen.

Z stack sweep through


A quick and simple way to show internal structure. Pick a colour scheme, the LUT ( look up table ) menu has some interesting options or you could simply colour according to emission wavelength.

With the '2D' tab active, select File - Export and go for 'Full resolution image window', set the compression ratio to 100 ( full quality ). 'Video for Windows' gives you a .Mov file and 'Quicktime' an .Avi


3D Rotation

A simple spin animation can look great in a presentation. If you go to the 3d tab in Zen, there are several rendering options. I'm using 'surface' which attempts to render a solid looking object. Transparent and maximum might be a better choice for a multi channel image.


To make setting up easier, under the 3D tab there's a slider marked Precise - Fast, setting it for fast will give you a much quicker refresh rate when positioning your object on the screen but remember to set it back to precise for the final render.


The key parameter to fiddle with is 'Threshold' which defines what pixel values count as solid surface - it's a bit sensitive and rarely needs much adjustment, between 1 & 3 tends to work well. The other settings are lighting controls that determine the overall look of shadowing and reflection in the image. The bars on the left and bottom of the image window control zoom and viewing angle.

Panorama setting

When you're happy with how it looks, go to the Series tab. For simplicity I'll use 'Rotate around Y', 'Start and Finish' allows you a more bespoke range of settings. I want the animation to last six seconds so at 25 frames per second I need 150 frames, you can also define starting angles and degrees per frame ( 'Difference angle' ) if you want control - I'm not fussy so I'm selecting Panorama for a full 360 degree spin. When you're done, press Apply then go away and get a coffee or two, your computer has many numbers to crunch.

The end product is a new image that appears on the right tab, you can view it using the same controls you use to run through a Z stack but the software hasn't saved it yet. You can save as a standard CZI if you want to access it in Zen again but more usefully you can export it as a movie file - As before go for the Full Resolution Image window option then select your preferred output format. When it's done, press play, sit back and enjoy.