Welcome to the second week of Cinemax, the course on Introduction to Advanced Tomography. This week, we are going to discuss experimental cases that we are working with. We will start on reconstruction of 3D volumes, the methodology behind it, the mathematics behind it. Also, we will discuss the computational resources that are required in order to analyze and process tomography data. They can be quite computationally heavy, and we will discuss various strategies for handling these large volumes of data. That also means that in this week, we are going to work with the actual data representing the experimental cases. Cases we have two off, one of them is composite materials that are used for wind turbine blades. Composite materials, they consist of various types of fibers that are glued together with the resin. The mechanical properties of the materials are closely linked to the structure of these composite materials. So, what we need is to establish a 3D model of the structure in order to be able to model and predict the properties of the material. The other case is chalk, natural North Sea Chalk, which is not a technological material, but a natural material where we are interested in how fluids that can be either liquids or gases, how they interact with the porosity in the material. In both cases, both the composite materials and the chalk material case, we need a three-dimensional model so that we can simulate how the material will react for example to mechanical stress, and how it will react to pressure of liquid, for example, passing through the material at a certain flow rate. To get to such a 3D model, we need to follow a number of steps from the data acquisition to the final three-dimensional model. This workflow we call it or pipeline you may also refer to it as, is here presented by Vedrana Andersen Dahl, who is an associate professor at DTU Compute, the Technical University of Denmark. A typical analysis pipeline involving images and volumes, involves a number of steps and spans over a longer period of time, and it also involves a number of experts. Usually, we start by a sample, which is scanned. The data is then reconstructed so that we have a volumetric data, and then this volumetric data often needs to be segmented. Also, very often, we are interested in obtaining a mesh from this segmentation in order to perform some modelling. All of this is because we want to have some results about the samples that we have scanned, so that we can get some insight in how this object is working or how this object is what is it made of. So, when we have a sample, for example from the North Sea Chalk where we may have core drillings taken up from deep underneath the water, what we will do is that we will acquire data from that sample. That is, as we have talked about before in the first week where we make these projections, the shadow images so to speak of the sample. What we need to do then is go through this pipeline that Vedrana just talked about, where from the recorded projections generate a three-dimensional volume by 3D reconstruction. This is the tomography operation you could see. This is what we will learn more about in the coming lectures. As we go from the 3D reconstructed volume to the next step, we will do segmentation as Vedrana also mentioned. This is this process of taking our now 3D representation of the values say, contrasts, measures in terms of gray levels, distributed all this grid in the three dimensions. We now take a process where we group these volumes, soft volumes of our 3D volume, so to speak in labeled domains. This is the process we call segmentation, and then we are still in three-dimensions, but we have now reduced the level of complexity by grouping into certain colors you could say, or labels, or identities. This segmentation step is then followed by a meshing step. Depending on the model we want to use, we will do this either in 2D or 3D. We can choose either to work with the complete 3D volume or we can choose various arbitrary slices through the volume depending on what type of model that it is we want to apply. The meshing step then will create yet another type of grid where the properties of the 3D segmented domain is represented in the nodes of this mesh. This is then the starting point for the last step going to the modeling where you can choose various forms of models to work with. In this course, we are working with the finite element modelling, and the purpose of this modelling is to get the resource on the actual material properties that we are looking for. So, again, citing the chalk case, what we are talking about here is for example, getting the parameters that will allow us to determine a single number for example, which could be a permeability. How well does a fluid pass-through this object with a certain porosity that we have modeled and segmented and meshed into a representation that shows how the porosity is distributed in volume, or it could be for example, the composite material case where we can see how this segmented meshed representations of our 3D structure will react to mechanical stresses that we apply to the model in a simulation using this finite element modelling, and see how the material structure reacts, and from that derive for example, the Young's modulus or other mechanical parameters for the material. All of these steps of course, going all the way from the data acquisition through reconstruction, segmentation, meshing, and finally modelling, are steps that are typically not mastered by one person that covers all of the entire pipeline, and that is why also in this course, we have various experts in the different fields. The various steps along the pipeline that will present them to you and show you how they are applied. Oftentimes, when working with problems like this, one will also work with these experts on the various steps of the process to get to the final result. To summarize, the workflow, the pipeline, we go from a step where we are taking data from our sample, data acquisition, the scanning of the sample. This we covered in week one where you were presented with the various tools for taking data, be it at a synchrotron or an imaging facility, then we get our projections and we do the reconstruction of our 3D volume to get to the tomogram. This can happen either at the facility where the data is staying, but it can also happen in your home laboratory when you have gotten home with your data. This is what we are covering in this second week of the course. When we got our volume, we move onto the segmentation and meshing, and this will be covered in next week. Finally, the segmented and meshed representations of our volume is then modeled, and this is what we will cover in the final week of the course.
