Introduction to the Micro-CT

[Music] welcome to the micro-ct video i am michelle Plue I work in Duke University's shared Materials instrumentation facility Micro computed tomography or micro CT allows us to see what a sample looks like both inside and out we use x-rays to visualize differences in the density within a sample to produce a detailed 3d image or model the x-rays do not damage or alter the sample the Micra CT is the same as a hospital CT or cat scanner but this technique can achieve much higher resolution on small samples first let's talk a little about safety the micro CT is an x-ray generating instrument and x-rays can be dangerous so the micro CT is shielded with let the lead shielding is also in this window so we can view our samples safely an additional safety feature is that the x-rays cannot be produced when the door is open finally x-ray safety training is required and regular safety inspections are made of the equipment because of all the safety features and protocols no extra protective equipment needs to be worn when operating the micro CT now let's discuss the operation of the micro CT we will be using a USB drive as our sample the micro CT generates x-rays by shooting electrons through a vacuum and hitting a tungsten target these electrons interact with the tungsten to produce a cone of x-rays that shoot out toward the sample sitting on a central stage when the x-rays reach the sample some are absorbed by the sample and some are trans mitad through to a detector the detector is like a digital version of film and sends the image information directly to the computer monitor darker areas in the image are where x-rays are absorbed by the dense areas of the sample brighter areas indicate regions where the x-rays pass through the sample however in the final reconstructed cross-section images of micro CT data this black and white color pattern is flipped so that white areas represent dense and black areas represent less dense material this is much like what you would see in an x-ray at a doctor's office size is a limiting factor for the micro CT samples wider than 25 centimeters will most likely be too big to fit in the entire field of view of the CT scan the stage that holds the samples in the micro CT spins around while the rest of the equipment stays stationary this is unlike a CT scanner in a doctor's office where the Machine wraps around a patient because the stage spins everything needs to be carefully positioned in order to stay in the field of view a sample positioned close to the origin of the x-rays or target will have a better image resolution 3 to 5 microns is the maximum resolution possible by our micro CT smaller samples allow for scans of much higher resolution as they are able to be positioned closer to the target this is comparable to shadows on a wall the closer and object is to a light source the more magnified it will appear on the wall once we have a sample positioned on the stage we can go into the software to adjust the x-ray energy the exposure time and the sensitivity of the signal to get the best image possible thank you for joining me for this video on the basics of micro CT imaging you [Music] welcome back I am Michelle pluie in this video we will discuss sample preparation for the micro CT the micro CT can be used to image a wide variety of samples unlike many other procedures it does not destroy the sample this makes the micro CT a very useful technique to analyze samples that are very precious and rare in the next segment of this video arianna will be presenting she is a graduate student at Duke University Ariana will discuss her samples and show you how she prepares them for imaging on the micro CT today I'm scanning a number of fossil bones from ancient primates called omomyoids there were relatives of modern day monkeys apes and a primate group called the tarsiers these fossils are from more than 50 million years ago and were collected in the balance of Wyoming by paleontologists from the University of California Museum of Paleontology scientists are interested in studying these omomyoids because they were one of the first true primates and studying their Anatomy can tell us about what kind of animals they were and how they lived studying ancient fossil primates can ultimately tell us about how primates separated and involved from other mammal groups I scanned the fossils in batches of many bones per scan I put many fossils into one of these small containers essentially just empty pill caps and place up to four pill caps in a single straw because each fossil bone comes with a unique specimen number used to track what it is and where it came from it is important to make and create a careful map of the specimens before I pack them the reason why we use pill caps and straws is because the specimens are very small and you want to get them packed in as tight of a space as possible so that we can zoom in as close to the fossils as we can while scanning these materials in addition to the cotton used to surround the specimens are all much lower density than the fossils which help them stand out during data process thing I also put many fossils in each straw because I have hundreds of fossils to scan and scanning them one at a time would not be very efficient this is another benefit to using the micro CT large batch scans can be done without sacrificing the quality of any individual specimen each pill cap with a fossil is filled with the cotton which is used to keep the specimens separated from each other and to keep them from shifting around during the scan unintentional movements of the specimens while scanning will ruin the quality of the CT scan and make it blurry each straw is then placed in a glass file with some clay around it so that is easy to position the straws right in the middle of the scanner stage the straw is held in place by the clay to reduce any vibration from the stage that might lead to unintended movement of the specimens many types of samples can be analyzed in the micro CT not just bones and fossils our instrument has been used to image USB drives electronic circuits museum specimens marine species plants and meteorites sometimes the samples need to be altered to get the best outcome with the micro CT an alteration to a sample may be as simple as taking them outside of any liquid in which they may be in such as ethanol or formaldehyde removing the liquid component will help decrease the noise in the acquired images because micro CT creates images based on the density of the sample very dense items such as rocks may not produce good images removing any unnecessarily dense features of the sample whether metal screws rocky matrix or thick packaging will also improve the scanning outcome similarly samples must have areas of different densities to produce good images the best resolution is achieved when specimens are packed in a low-density container that spins tightly around the center of the stage orienting the longest dimension up and down keeps parts of the sample from being cut out of the field of view when the sample rotates around 360 degrees opting to stained soft tissue samples with a solution of iodine for example can increase the level of detail detected by the micro CT here is an animation of a tree shrew from a museum collection it is about 15 centimeters long this shrew has been treated with an iodine stain in order to perform a virtual dissection without ever cutting into the specimen the researcher can visualize muscle and soft tissue details inside the shrew that are highlighted by the stain thank you for joining me for this video on micro CT sample preparation welcome to the image processing portion of the micro-ct video i am michelle plume CT scans produce large data files that can be up to 20 to 30 gigabytes in size the first type of data that the micro CT produces is the raw projection data this data is a series of thousands of x-ray images taken around a single rotation of the specimen shown here is the video of thousands of x-ray projections for a honeybee scanned in the micro CT a computer then uses the projection data to reconstruct a final set of images that shows the three-dimensional detail of the specimen the reconstruction data comes in the form of a stack of TIFF or DICOM images that depict the sequential cross-sectional structures of a sample from top to bottom this stack of images is also called a Z stack the Z stack of the bees shows not only the external but also the internal anatomy of each cross section the Z stacks can be used to virtually inspect measure and illustrate the overall anatomy of the specimen the Z stacks are loaded into software where they can be visualized in 3d and specific ranges of grey values which represent different densities or materials can be labeled these labels can then be turned into 3d models and animation here a 3d surface is made of the exterior of the B if you were to digitally slice through this model you would still find all the internal anatomy depicted in the Z stack 3d models can then be sent to a 3d printer to create a physical representation of the original sample 3d printed models can be scaled up for easy examination of the specimen and put on display without worry of damage to the original because of the non destructive nature of the micro CT and its ability to visualize structures that are otherwise difficult or impossible to see it has become a popular tool in many fields of research you've already seen some examples of a USB and its internal circuitry being examined of animal muscles and skeletons being scanned and of fossils being digitized the micro CT can be used to illuminate delicate structures like the intrusions of roots in soil the less dense materials like the roots cutting through the core are colored in blue while the more dense pebbles and dirt are in oranges and reds the roots can also be isolated and studied as if they were suspended in air the above examples are only a small slice of the types of research that used the micro CT some other interesting applications include work on mummies paintings archaeological artifacts and much much more arianna will now show you how these different kinds of CT data are created for fossil samples I use the micro CT scanner to study these fossils because there are very small animals some of them were only the size of a mouse small animals have very small bones that are difficult to describe and measure using just a naked eye there are also more difficult to handle and easy to lose track of which can be extremely stressful because fossils are irreplaceable using micro CT scanner lets us make a digital copy of the fossil so that we can virtually manipulate it we can blow it up to any size on the computer so that anatomical features can be more easily seen and measured and the CT scans help us preserve an archive these fossils digitally in case a fossil is accidentally lost or broken in the future after a specimen has been scanned and reconstructed I use to program to process and visualize the data the first program I use is a free program called image J where I crop the stack of scanned images to make the datasets smaller and more manageable and so that I can separate out and better keep track of many fossils that I have included in the single scan I do this by opening the TIFF stack and image J selecting the area of interest and selecting crop I then save this new image stack with the specimen number and a file name next I produce virtually reconstructed 3d surfaces of the skin the fossils in the 3d visualization program aviso in a visa I open up the TIFF stacks of the images I just cropped an image J I select the volume of interest using a specific tool in the program and do a smoothing steps to decrease the noisiness of the 3d model and produce high resolution surfaces for looking at on the computer or for 3d printing ultimately I'll upload these scans to an online repository for such data morphus org so that other researchers can look at the same specimens without ever having to pull a fragile original out of the museum drawer

Channel: Duke University - SMIF

Views: 22,250

Keywords: MicroCT, Duke, Duke University, Engineering, Clean Room, Nano, Characterization, CT, X-rays, Coursera, UNC Chapel Hill, NC State, Micro-CT, SMIF, Tutorial, Nano-Characterization

Id: apM_M5YRFGI

Length: 16min 34sec (994 seconds)

Published: Thu Nov 09 2017