Stochastic modelling of microstructures
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Leibniz MMS Days 20241 / 17
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Transcript: English(auto-generated)
00:05
Thank you, so thanks for the introduction and thanks for the invitation and the possibility to give an overview of our work here As I learned that the audience is pretty wide I definitely decided to give a broad overview to show a lot of different topics at the cost of
00:24
Not being able to show all the details, but I will give reference to all the papers You find the complete links on my webpage and you can check the details there Also, I have to say that this is a joint work with a lot of people mostly from my group here at RPTU and from the Fraunhofer ITWM
00:45
I haven't listed them here. You see the names in the references and here a global thank you to all of them It's a pleasure working with you What I want to show is different projects that we have worked on different ways of
01:01
Including stochastic models for micro structures in the design and analysis of materials So as you may all know nowadays materials are really tailor-made for particular applications and the micro structure is a very Important contribution to tailor the performance of particular materials
01:26
Similar things also apply to what I call natural materials here So things that apply appear say in the body like bone or tissue or blood vessels in an organ But also in materials like wood and even in polar ice
01:43
If you want to learn something about the micro structure Quantitative analysis of image data is an important source of information Mostly we go for 3d imaging for instance by micro computed tomography and we can derive a lot of geometric characteristic of the micro structure to in first place
02:04
Describe what it is that we are seeing to compare micro structures So to say what happens if I change the production parameter? What happens if I apply some load to some sample or in the medical issue? What is the difference between?
02:20
Healthy and a diseased tissue or organ and furthermore geometric characteristics that we have something like Size distributions direction distributions can also be used to fit stochastic models to the micro structure Here are some examples if you don't have a clear picture of what I mean when I say micro structure here
02:44
You have some of these engineering Materials from ranging from foams over fibers porous filter media concrete and some natural Examples blood vessels in the liver airways in the lung and the pore system in polar ice We will meet most of them again during the talk
03:03
How do we get our data well in material science established imaging procedures are scanning electron Microscopy here an example of a scan of a fibrous non-boban material microcomputed tomography when it comes to getting 3d data here a sectional image of a
03:24
fiber reinforced polymer and Focused ion beam serial sectioning scanning electron microscopy where you combine serial slicing of the sample by a focused ion beam and then taking an SEM image in each step such that you can stack all the 2d images to get a 3d volume that you can then analyze
03:49
When we want to motivate why we work with stochastic models for the micro structure we usually show a kind of workflow such as this and the One of the main motivations is to be able to do virtual material design
04:04
So over here we start with the sample that we already have we say pass it through a CT to get a 3d image we Process and analyze the image to learn something about the microstructure We may have additional information on the production process on the geometry that we have
04:23
That gives us information like which model class we should choose Then we fit model parameters to try to mimic this initial sample as closely as possible And then we can simulate Some properties. So for instance here what happens if I apply some compression on a form sample
04:43
The nice point about the model is that by changing the model parameters I can virtually alter the microstructure and I can investigate a lot of different Microstructure geometries and by repeating cycles here of changing the microstructure Investigating say compression behavior. I can learn something about what are beneficial properties of the microstructure for particular
05:07
applications To Give some example of this. I will start talking about virtual design of foam structures So foams are a really broad glass of materials and we have had a lot of projects on those
05:23
Even foams can come in like very different shapes. So here on the left hand side We see that what is called an open foam So basically some interconnected network of struts on the right hand side You see a closed cell foam So basically planar walls separating the cells of the foam and in the middle you have something like a hybrid
05:45
So you have both open windows, but also some planar structures in there and Again due to the wide range of applications a lot of properties are of interest mechanics permeability
06:00
Heat transfer all those can be modeled in foams and it depends on how this cell and strut geometry looks like How do we model a foam well our most important ingredient is a model for the cell system and here we use random Laguerre tessellations here a 2d illustration of how such models are constructed
06:22
This is what we call a Voronoi tessellation So you have a set of points the black dots that you distribute randomly in space and then each of those points forms a cell consisting of all points having this generator here as nearest neighbor in the set of the black dots and
06:41
Then what you see is if you change the point pattern So here it's a bit more disordered than what we see here that has an influence of the size and shape distribution of the cells that you can produce If you want to have even more control you can start assigning some weights to the point So the X I here are the black dots and now the RI are some positive weights
07:05
Which are drawn as radii here around these points and then you see those are the exact same point patterns But the cell sizes are shifted in favor of those Balls having a large radius they grow larger cells. Whereas those grow smaller cells
07:22
So that gives us more control and If you are interested in how exactly those cells are defined so you would minimize the distance Voronoi It's just Euclidean distance And here we have a weighted distance looking like this That gives us the Laguerre tessellation a model also with with convex polyhedral cells And of course we do that in 3d for our forms
07:43
The model fitting procedure then works as follows. We start with a real foam We use some morphological procedure in our CT image to separate all these cells here to be able to analyze Characteristics of their size and shape for instance, then we fit a Laguerre tessellation
08:02
So we want to make it as close as possible to that observed cell system and then for an open form for instance We would just take the edges of the tessellation cells and then put some volume on those giving us structures like this What are ingredients that we can include in our model Well, of course the cell system so we can change size shape and also regularity of the cells by regularity
08:27
I mean somehow how roundish they are and how similar in volume or in size And for the struts we can control the thickness if you look closely at the real form You see the thickness even locally varies
08:42
It's not completely constant throughout the strut and also the cross-section shape. So here we have circular cross-section here We have a triangular cross-section You can decide to include some closed walls here to have these partially closed forms And if you want you can introduce some anisotropy by elongating the cells or by deciding that these closed walls
09:03
appear at some preferred directions In The project math bits we have looked at the design of foam filters for cell Chromatography this is a procedure that is used in Biomedical applications
09:21
so you have some suspension say blood and you have some cells in there and you have an application where there are some cells that you want to be there and others you do not want to be there and The idea is to filter those which is currently done with very complex processes our idea was that you have a glass column you put in some filter medium and you pump your
09:45
suspension through that You functionalize the surface of that material such that the bed cells like this functionalization So they try to get attached to the surface Whereas the good cells the ones you want to stay in the suspension don't care about this
10:01
Functionization and just flow through So that may look something like this So what we have in mind is we use our Laguerre tessellation model to produce a virtual material here We produce that by a 3d printing we put that in a glass column and then our cells flow there and eventually the bad cells are attached to the surface and
10:22
Caught from the suspension a Few words about the manufacturing so the challenge here that is that we need very fine structures because Cells are small things and we want them to get close to the surface of the material at some point So they have a chance to actually get caught
10:42
So here we decided to use these windows here of ten times the cell diameter resulting in roughly 200 micrometers and Printing was done here at RPTU by Eric Waller and to show somehow an idea of scale Eric donated a hair Here and put it on top of the structures. So they're really really tiny
11:05
Next thing we need to do is we need to understand the performance of the material and in first place We looked at permeability, which is the basic flow characteristic that we should be interested in So we did a simulation study where we fixed the porosity of our phones and we varied all these other
11:25
parameters that we have So we used the very same lager tessellation model. So cell system stays constant But we changed the strut shape. So we use the cylindrical and triangular ones We use the original cell system and a cell system
11:41
relaxed by practice surface revolver, that's a software that Tries to mimic the physics that happens in liquid foams So if you think of the foam that say you have on your beer it tries to form cells that are really nice Roundish and follow plateaus laws. This is done in that software and we observe that
12:02
Partly that gives us more realistic cell shapes We also included closed windows because we thought that might be nice to give the cells more room to Get stuck somewhere and we changed the fraction between 0 and 15 percent closed walls and
12:21
We also chose different closing mechanisms one is an isotropic So each wall is equally likely to be closed each facet or an isotropic where we thought that probably we should Put the closed walls just in the way of the cells. So we rather put them like horizontally if the cells come that way
12:41
We had 20 realizations per setting and then we computed permeability using the software geodict as Some aim we wanted to explain the permeability using certain Characteristics we have seen similar applications in previous talks
13:02
We were building on previous work by the coupon on the west of and others who found out that some characteristics called tortuosity and constructivity are well suitable for explaining that Tortuosity somehow measures how winding path through the pore space are and
13:21
Constructivity is a measure saying like how Bottleneck-ish your structure is so is it a straight pipe or is it something that shows a lot of variations in thickness? and We fit a regression model and initially we thought that maybe we need different models say for circular and triangular
13:41
Cross-section shapes, but it turned out that actually one model was able to handle all the cases that we had in the study So what you see here is tortuosity Basically given across cross-section shape explains the behavior here So in the colors you see different directions, so we also looked at an isotropic behavior
14:04
So we had permeability in different directions And we had the an isotropic and the isotropic Closing behavior. Everything is presented here And then we have basically two groups one for the circular cross-section one for the triangular cross-section
14:21
And they were nicely linked if we took constructivity as a second explanatory variable So this way we now have an understanding how our particular Generation mechanisms influence the permeability. So here I should say we use the Darcy number which is like a Dimensionless version because we are using virtual volumes where the length unit is basically arbitrary
14:48
Okay, so Here what I have shown you is an example of this cycle. So produce a lot of different microstructure and investigate some property of those Looking at that picture. It looks a little bit like
15:01
Analysis is a prerequisite of modeling which is of course true Now I want to show you that modeling also supports analysis So as one example, we will be interested in looking at branching points in microstructure coming back to our foam
15:20
We can again see an open foam Consists of a lot of interconnected struts. So that's an example of a multiply connected network We have further such examples for instance poor spaces in microstructures that are also often modeled as networks or if you think of our mouse livers blood vessel systems also behave like this and
15:46
It is of interest to analyze the connectivity of such networks and for that we make model assumptions We say okay what we are looking at is something that is locally cylindric. It's somehow put together by cylinders and At the branching points the structure is a little bit thicker than along the cylinders and using that information
16:07
We were able to design a morphological algorithm that Segments all these branching points. So these greenish dots here from the microstructure This has been used for foams so for instance to look at the
16:22
Strut length distribution strut orientation distribution also the cross-section shape variations along the struts But we also used it as I said for blood vessel systems. So from our medical partners We got some synchrotron images of corrosion casts of mouse livers there You would pump some polymer into the blood vessels and then you would image that
16:45
Polymer structure that you get rather than the original tissue And we were looking at a disease called fibrosis Which may of course appear naturally But they all have also some tools to induce that in the mouse So what we see here is a healthy liver and what we see here is
17:05
Samples of livers where that fibrosis has been induced by two different mechanisms While this still looks pretty close to that you see there is a severe change of blood vessel morphology there And if you want to measure to which extent things change
17:21
What you could do is apply our algorithm and look at branching points In in this vessel structure and if you compare the thickness distribution in these connection points you see that The more severe your disease is the more the connectivity goes down
17:43
So there is much less branching points here than there and also the variation of thickness in this points increases which Corresponds to this visual effect that you have much more variation and blood vessel thickness in this right sample compared to the other ones
18:00
Another application from clashology is We looked at CT images of ice Samples from polar ice cores drilled in Greenland or in Antarctica so this is a Greenland sample and What you see is if you visualize the pore space so here ice is not a solid block it's ice and
18:25
complicated pore space in there we look at film which is something in between fluffy snow and compact ice and If you look through such an ice core Which may be so ice thickness in Greenland is something like 600 meters in Antarctica
18:43
It may be several kilometers thick and if you go to deeper in the ice you see that porosity decreases and connectivity gets lost and We found that also by analyzing the branching points. So here are four different depth
19:00
so a back this unit is roughly half a meter and You see the deeper we go The less branching points we see and another thing we see if we go an xy direction Which is the deposition plane everything is nicely homogeneous and constant So what we do here is we take such slices through the volume and observe points per slice
19:23
So if we slice like this or like that everything is constant if we slice like this, that's the black line We see a lot of change That's not only an indication of gravity acting but also an indication of seasonal layering going on in the ice so if it snows in winter and it snows in summer, that's a
19:43
different behavior of the ice that you get from that So we see these tools So using image analysis with your rather broad model assumptions gives us some Way of analyzing very complex microstructure and you see they came from very different fields
20:03
So it's not so important what it is, but which geometric assumptions we can make Another example that may be of interest for the audience here is analysis of fiber systems So here we will be interested in the fiber length distribution
20:21
So if you look at glass fiber composite You don't know what exactly the length distribution is because fibers break during processing so you can't like measure them before and then know what is in but it may differ due to processing and it would be interesting to get the fiber distribution from a CT image an
20:41
Established procedure is for instance an ashing test where you would burn the structure and then see which fibers are coming out We want to do that from CT If you want to analyze a distribution of something you would usually say, okay, I measure some of them So give me a bunch of fibers measure their length and then we look at the empirical distribution
21:03
So if I was able to tell all the fibers in an image apart I could measure the length and then look what the distribution is The problem is that the estimation is hampered by edge effects If you look closely a lot of fibers here are cut off by the edge of the window and we don't see how long they
21:22
actually are They are at least that long but the true length is unknown and that must be taken into account in the analysis So a classical approach is Sampling by re-weighting so-called Meisel-Lante-Joule approach So if I have some fibers
21:41
What I would do is I keep only fibers that are observed completely with that I avoid that censoring. So here I don't know what the true length is. So I throw that away However, that way I also get a sampling bias namely Longer fibers are more likely to be hit by the edge of the window than shorter fibers
22:04
They fit in much more easily So it's a higher chance of observing them than the long ones and that must be taken into account And this is done here by some re-weighting The problem is still I lose most of the fibers where they still provide some information
22:21
Knowing that this fiber is that long in the visible part I already know that it can't be as short as this one and We would be interested in taking that information into account in particular as I said is most of the fibers may be intersected by the edge and Here we found some approach by a Swedish group who
22:43
investigated this for wood fibers in 2D and we extended this approach to 3D and to also cubical observation windows Some ideas so here that's a parametric approach. So we assume that our fiber length distribution is log-normal
23:03
And We call L tilde the visible length. So these are the length of these parts that we see Complete fibers or probably not L is the actual true length So this is how long the fiber was before it was eventually cut off by the edge of the window. That's
23:22
The thing we are after Statistically what we do is we take an expectation maximization estimator So the idea would be I know that I saw fiber of this length, but it may be cut So I'm interested in what do I expect how long it actually was? So this is what happens here. And because we are log-normal we take the logs. So here we are talking about normal distributions
23:47
And the idea is like this so we are after this how long is a fiber given the part that I see This is unknown What we have is this we assume how long the fibers actually are and
24:03
Given our placement and our window cutting mechanism We know if a fiber is that long how likely is it that I see a certain part of it? So this is kind of the forward problem, right? I take fibers. I put them in and I see what I get and Base rule says how do I get like the inverse thing? What do I see? What was there and
24:26
This density can be computed it's a lot of like Geometry and probability going on and having computed that we can sample from that expectation and eventually get the parameters You can prove a lot of things that statisticians like to prove so the estimator has nice properties and
24:46
In a simulation study we found acceptable results already if the fiber length at the edge of the window were of comparable size Problem is if you want to use that you need to tell the fibers apart in the image and
25:02
Here that seems doable here probably not so well the problem is as we saw there is a trade-off between field of view that you have in a CT and the Resolution if you want to have a high resolution so you can tell the fibers apart you make the window small
25:21
Which means a lot of fibers are cut so that's a problem and Then we thought about alternatives We thought what if we do not just need all the fibers, but just the endpoints and Michael's golden bag at ITWM considered in his PhD thesis an approach for finding the endpoints of such fibers by looking at local curvature and
25:46
the question is is that statistically useful and Now we built a really Heavy model assumption on our process, so we say okay, let's distribute fibers randomly in space all fibers independent of each other
26:01
Practically, that's nonsense right fibers to interest to interact they can't intersect for instance But here we need a strict model assumption to be able to do computation so assume for a moment We do that we do it in 3d here. I just painted 2d So this is what we get then we have the endpoints so the greenish things over here
26:21
And now what we do is we throw away everything else We do no longer know which points come from which fibers. We do not know how they are connected. We just know the points Can we get the length distribution from that and the answer is yes? The nice point is that if we use that model
26:41
There is a thing called replace K function, which is a very standard statistics used in point process statistics Everyone is using it there and the nice point is for this model It has a closed form solution. You can write it down and as the fiber length distribution Of course is one ingredient in this point process. It must appear in that K function
27:04
which basically says something about how often two points certain distance apart a core and So what we can do is we can estimate our K function from the observed endpoint pattern We can solve it for the direction distribution basically meaning we estimate a histogram of that distribution and
27:23
Then we get what we wanted and here is the result of a simulation study. So we had a lot of fibers we take only the endpoints and here in the circles You see the distribution we put in if we just use the endpoints
27:40
You see you get a problem with the longer fibers if you additionally put in some information on the fiber direction distribution Which is usually easy to get You get a very nice result So so far this is still of say academic interest we haven't put that into practice, but I thought it's a nice example showing how
28:02
very heavy model assumptions allowing you to do analytic computations can Compensate a loss of data that you have. Okay, so we just learned that models are also useful here in the analysis Next point is if you want to analyze a sample you actually need to process your image first
28:24
So one main question is where is the component I'm interested in so in the next step we want to look at image segmentation and As everyone is using AI nowadays, we also look into that and we see how our models are helpful there
28:41
So usually you are imaging like a computer tomography gives you gray value images We need segmented images. So we need to say where is the foam structure? Where are the fibers? Where are the grains? If it everything is nice and easy like here thresholding We do the job everything that is brighter than a certain value is set to foreground
29:05
so We do like this job is done But we may have structures where it's more complicated. For instance here. We have a sample of a concrete with crack Obviously the crack is dark But you see there is a lot of air points that are equally dark
29:24
Right, everything is filled with air same absorption contrast equally dark So just doing a thresholding will not do the job because it gives us both pores and crack How can we distinguish the crack from the pores? generally in such tasks there are
29:42
Two things that you could consider one is you look at an image and you want to decide is there a crack? Yes or no? We don't Investigate that here Alex will show you an example of that. We would rather be interested in crack segmentation namely finding all the pixels that belong to the crack
30:01
as I said simple thresholding does not do the job and if you look into the literature problem that is studied probably even more often is Cracks in road pavement because that is related to automatic inspection of road quality Why are we interested in concrete? Well, we have a large-scale CT device currently under construction here at RPDU
30:27
the device is called Gulliver and The idea is to be able to have in-situ scans of concrete beams under load And we have seen here mechanical tests of small samples here
30:41
We are talking about concrete samples of up to six meters length And we are supposed to scan them here leading to enormous image sizes that we have to analyze Well, we were interested What are people doing to segment cracks and there is a lot of different methods around one is classical filters Where you basically look at the shape
31:02
Crack is a planar structure most thin and planar This is done in this filters There are methods based on template matching where you have a planar template which you move over the image And you say where are locations where my image looks like that my template There are region growing approaches that are based on the assumptions that cracks are connected
31:25
Structures and this can also be used in path-based minimal path space a crack is a connected dark structure That's the idea in these approaches here. And of course there is machine learning. So here we took random forest and Neural networks or the established unit into account now, we would be interested in which of those methods work best
31:49
well and Probably and one of our reviewers asked this why do you take these classical methods into account nowadays? Everyone is doing machine learning. Why do we even bother to look at that other stuff?
32:04
Well one important point is the classical methods do not require training right you make your model assumption and they work right away So they can be immediately be applied if you have the right model assumptions So here again model assumption is basically cracks are locally planar
32:22
So here we just see them in 2d, but they would go on over the structure and they are dark That's what we are using. Of course scale parameters need to be chosen So we'll see it matters how thick the crack actually is and in our study among the classical ones Hessian based percolation and among the machine learning methods unit what gave the best result
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How can we tell that I mean, how can we say what is the best result? No one knows what the truth is right and here our models come into play So how can we assess the accuracy and how can we even train machine learning methods? We need some training data, right? So we use our models because manual annotation is not really practical
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So you can't really have someone sitting down and painting each correct pixel in your image So we use semi-synthetic images The idea is we simulate a crack by a suitable model and then we superimpose the crack with some real concrete Background so we do a CT scan of an image without crack. We superimpose that and that gives us a
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Crack image where we know exactly where the crack is Cray value distribution is chosen similar to pores because we know both is filled with air How do we get our cracks? So here we developed a model based on boronoi tessellation again because we know how to deal with these
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So basically we take the facet system this time and we solve a minimal surface problem to determine a particular Facet system in the tessellation and this is the template for our crack Here are a few example a thin crack to a little bit thicker cracks cracks of
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Varying thickness all this is possible with our model. They can branch they can overlap you can rotate them and we have generated a system of Images with cracks of different sizes different shapes on different backgrounds with different levels of noise
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which is published under the name boronoi crack 3d in cenolo and Using these data we can now successfully train the machine learning methods and we compare the results Here is an example. So here is our ground truth Here is the result of the different methods if you wonder why there is this funny hole here
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Well, here's something like this happened Our crack was intersecting a pore and then of course, it's not locally planar anymore and the methods just miss it Now I said cracks are multi-scale structures, right? So they change in thickness and you see already down here very thin cracks for instance, maybe an issue
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So, how do we put that scale into play? well, one typical thing is that you have a an algorithm that can deal with cracks of a certain thickness and then You can either use several scale parameters and run the algorithm multiple times or you downscale your or upscale
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Usually downscale your image run the algorithm multiple times and then combine the results That works but of course increases runtime as you have to run the algorithm multiple times Here you see an example you see you can even get from very thin to very thick cracks here
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We still had some issue with fibers that you see here, which are also dark. So this is something we should work on But we thought maybe there's a more clever approach why not change the structure of the network and here a very good idea of Tinbarishan was that he replaced the finite window
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Convolutions that you usually have in neural networks by at least transform which is also a convolution But with a different kernel and the nice point about the least transform is that it's scale Equivariant so if you rescale and then transform or the other way around it doesn't matter That's not true for finite window convolutions where things may enter your window or exit your window
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then they are gone or there and This way you get scale invariant networks. So here we have a huge crack We have trained on crack with three Three pixels only this is a rescaled unit segmentation. This is the reason it so these net can
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Generalize to unseen thicknesses due to the scale invariants The next challenge we want to tackle is that well concrete is not just concrete There's a lot of different recipes a lot of different ingredients and we have to have methods that are robust to that changes
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and Characterization of crack morphology is then of course also an issue Finally an example where we are interested in fib SEM imaging This was this serial sectioning thing here. You have the problem if you have a porous structure
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So now we are on a different length scale CT is on the level of microns here have we have nanometers We have shine through artifacts. So if you look on the top of a porous structure, you can look into the pores So not everything that is bright here is actually on the uppermost layer It can also be a little bump somewhere down in the pore
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So if I gave you a pen and asked you to draw what is uppermost layer. I Well, we use unit again Again, we need training data. And here we have an approach for
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simulating synthetic SEM images. So what we have is micro structures based on balls and cylinders and Tobin will develop some approach for mimicking the electron-matter interaction in the microscope Using the library monso2 and he
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looked at a lot of methods to accelerate because a lot of electrons have to jump around and he made that possible in like doable time But still doing one such image takes something like several hours to run even if you do that in parallel for the slices If you need a lot of training data, you should speed that up. So what we looked at is a
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machine learning approach learning from a few of these Physically correct simulations then to then speed up the image generation. So here we use the restaurant as a rugged model and The one of the key points was to find a correct or a suitable data representation
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so we do not work on the 3d volume images, but rather a representation of these structures as height fields and normal maps Now the runtime is roughly 200 microseconds per slice. So now it's really really fast and
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it even generalizes so we trained that and balls and cylinders and then we applied it to a structure of cubes and It looks reasonable. So here is what we got with the physical correct simulation. This is what the Snet gives you You might see noises missing. So this has to be added manually But here is the residual and you see up to some slight problems over there. It looks really nice
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Now it's not only submitted. I learned this week that it has been accepted for the synthetic data workshop at CBPR So to conclude a quantitative analysis of image data yields a lot of important information on
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microstructures models from stochastic geometry Can be used as prior information in the image processing and analysis you get ground truth data for evaluation of whatever algorithm you apply and for training machine learning approaches
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For image segmentation, for instance, you can reproduce characteristics observed in micro structures Also, you can use the models to generate samples larger than the ones you are able to observe using your imaging technique Of course also with altered microstructure and if you combine that with numerical simulation of my macroscopic properties
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You can learn something about microstructure property Interaction and that paves the way to a virtual design of materials Thank you for your attention