Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography

Hello.My name is Michelle Ov from the Bats Lab at the University of Tubing, and in this presentation I want to talk about non-invasive three-dimensional visualization of the internal organization of micro AHR puts using synchrotron X-ray tomography with a submicron resolution. The model system that we're working with is the orbited mite Aus Long osis, a micro COLYER AHR output of 800 microns to one millimeter in body size. This is a picture taken from all lab culture where you can see the animals feeding on algae.

To study the internal organization of Argos, we use synchrotron x-ray radiation to produce tomographic VOX data at the SRF and Grable. Here you see a picture of the ESRF with the large storage ring and in the upper right corner you see the experimental hall of ID 19, which is located outside the ring For the measurements, samples were critically point right and mounted on plastic pins using super glue. The experiments were conducted at 20.5 KEV and 1, 500 projections were taken for the reconstructions.

Here you see the camera with a co freelance CCD chip, 14 bit dynamic range and four megapixels. The simulator shown at the bottom of this picture translates x-rays to visible light. This is a closeup on the sample holder and the rotation table.

The sample is mounted on the Goya meter head to enable a proper orientation of the sample in the beam. A detailed description of the experimental setup is given in our 2007 paper in the Journal of Microscopy. In this presentation, I will focus on data analyzers with respect to three dimensional visualization using the software Fiji Studio Max.

First, I will show you how to remove the gray values from the background to extract the sample information. In the histogram, you see one large peak, which belongs mainly to gray values from the background. After removing this peak from the histogram, you can see the sample coming out of the gray cube.

Next, I will show you how to rotate the object using the key framer VG studio. Max has a set of predefined camera trajectories. Here I use the XY circle to generate rotation around the vertical Xs, and this is the final animation.

The large structure on the backside of the animal corresponds to the surface of the super glue. Now I'm going to show you how to set a virtual cutting plane to be able to have a three dimensional look into the internal organization of the sample. There are three orientations where a cutting plane can be set frontal actual zeal.

Here I use the frontal plane and find a cutting position somewhere in the middle of the animal, in the region of the, this cutting plane doesn't have to be static. Again, using the key framer, it can be moved along any axis. In this example, I use the preset clip Z to move the cutting plane along a longitudinal axis of the sample, and this is how the final animation looks like step by step, you can see and follow up the 3D organization of all internal structures with a P resolution of only 0.7 microns.

Besides the predefined camera trajectories, it is also possible to generate user specific camera paths. To do this, choose the free camera look at mode and adjust the camera and the focal distance of the virtual lens to any desired position. Step by step, new camera positions can be defined to follow an individual path of any complexity.

The 3D window in the upper left shows the effect of all camera settings in real time. The final example takes you on a virtual flight following the complete digestive system through the animal. Here you see some parts of the gma, the colliery, the labrum, and the rotella.

We're coming closer and enter the mouth of the animal. Here you can see the PHNs on the dorsal side. Now we're passing through the esophagus to enter the ventriculars.

Our riveted mites have two large ker. These are slike structures with digestive function. We enter the right seum.

Through its small opening, you can see numerous IDE cells. These play an important role in digestion, although the complete function and mechanism is not yet completely understood. Returning to the ventriculars, we see a particular structure, the Isal valve through which we actually entered the ventriculars a minute ago, right at the border of the ventriculars and the colon.

You can see a food bull, which is compactified and surrounded by atrophic membrane. Behind the food bolus, you see a fecal palette. We are flying through this FE palette right now.

Afterwards, we passed the short inter colon and enter the post colon. Here you see the large and characteristic microbially. Finally, you can see the inner surface of the particular animal plates here, just like a fe palette.

We leave the digestive system. Now we have a short final look on the exterior ventral side of the animal and see the an animal plates, the AAL plates, and the genital plates.