![The Virtual Paleontologist](/img/default-banner.jpg)
- 32
- 136 480
The Virtual Paleontologist
United States
เข้าร่วมเมื่อ 23 มิ.ย. 2020
Paleontologists have embraced the use of X-ray CT scanners, surface scanners, and photogrammetry to generate 3D models of fossils. These paleontology-focused tutorials for open-source 3D software are designed to introduce complete beginners to the world of virtual paleontology.
About Me:
I am a postdoctoral fellow in the University of Michigan Department of Earth and Environmental Sciences / Michigan Society of Fellows. I use 3D data for my research on the evolution of mammalian locomotion.
Funding to start channel provided by Tara Smiley through:
NSF Postdoctoral Fellowship in Biology - Biology Collections; DBI Award #1612002
Indiana University Environmental Resilience Institute, supported by the Grand Challenges Initiative
About Me:
I am a postdoctoral fellow in the University of Michigan Department of Earth and Environmental Sciences / Michigan Society of Fellows. I use 3D data for my research on the evolution of mammalian locomotion.
Funding to start channel provided by Tara Smiley through:
NSF Postdoctoral Fellowship in Biology - Biology Collections; DBI Award #1612002
Indiana University Environmental Resilience Institute, supported by the Grand Challenges Initiative
Merging Landmarks in 3D Slicer
For geometric morphometric analyses with a combination of curves and points, landmarking in 3D Slicer will create multiple files: one for normal point landmarks and one for each curve. I demonstrate how to combine point and curve files.
0:00 - Example points and curves
0:50 - MergeMarkups module
1:22 - How curve files are formatted
3:50 - Converting curves to points
4:26 - Combining markups with MergeMarkups module
4:54 - Recording which points are part of a curve
0:00 - Example points and curves
0:50 - MergeMarkups module
1:22 - How curve files are formatted
3:50 - Converting curves to points
4:26 - Combining markups with MergeMarkups module
4:54 - Recording which points are part of a curve
มุมมอง: 267
วีดีโอ
Exporting Landmarks from 3D Slicer
มุมมอง 1833 หลายเดือนก่อน
Slicer is a great tool for landmarking, but getting landmarks formatted for other software like R can be tricky. I demonstrate 3 ways to get landmarks out of Slicer. SlicermorphR Github: github.com/SlicerMorph/SlicerMorphR Python Script Github: github.com/aelkort/SlicermorphAddon/ Chapters: 00:00 - Option 1: Procrustes Coordinates from Slicermorph 02:04 - Option 2: SlicermorphR 04:43 - Option 3...
Mesh Tools in 3D Slicer
มุมมอง 1.1K10 หลายเดือนก่อน
Though 3D Slicer focuses on CT data, it does have some basic tools for working with meshes, such as decimating and mirroring. These can be useful for workflows that primarily take place in Slicer, so you don't have to switch software. The Surface Toolbox and the Dynamic Modeller are the two modules demonstrated. 0:00 - Surface Toolbox 0:56 - Clean 1:36 - Decimate 2:59 - Mirror 3:31 - Plane Split
Choosing Hardware for 3D Data
มุมมอง 34411 หลายเดือนก่อน
I have gotten asked if you need super expensive equipment to work with 3D data. The short answer is no not really and the long answer is this video. Items shown (Note these are not necessarily product recommendations, just examples if you are curious what I use): Laptop: us.msi.com/Laptop/Raider-GE66-12UX/Specification Desktop: www.bestbuy.com/site/cyberpowerpc-gamer-master-gaming-desktop-amd-r...
Geometric Morphometrics with Slicermorph
มุมมอง 1.8Kปีที่แล้ว
The Slicermorph extension for 3D Slicer includes tools for the preliminary steps of geometric morphometrics (GMM), including the Generalized Procrustes Analysis on 3D landmarks and visualization of the shape space. The dataset used in this video will be made available once my paper is published. More on GMM: morphometrics.earth.indiana.edu/ More on Slicermorph: slicermorph.github.io/ Acknowledg...
Measuring and Landmarking 3D Data with the 3D Slicer Markups Module
มุมมอง 2.6Kปีที่แล้ว
3D Slicer can be used to place points, take linear measurements, and create curves from both surface and CT scan data. The Markups module contains these tools, and I show how to use them. Acknowledgements: Thanks to the William R. Zooarchaeology Lab (WRAZL) at Indiana University and collections manager Jess Miller-Camp and to the University of Wyoming paleontology collection and collections man...
Importing Data into 3D Slicer with ImageStacks
มุมมอง 2.5Kปีที่แล้ว
I show how to work around Slicer's limitations with large datasets using the ImageStacks module to import data. This module comes from an extension Slicermorph. Find more information about Slicermorph here: slicermorph.github.io/ Acknowledgements: Thank you to curators and staff at the American Museum of Natural History, especially Ruth O'Leary and Judith Galkin for access to specimens. Morphos...
Photogrammetry in Meshroom | Generating Textured Models
มุมมอง 5K2 ปีที่แล้ว
I show how to use Meshroom to generate 3D models from photographs taken for photogrammetry. Meshroom - alicevision.org/#meshroom Acknowledgements: Thank you to the Indiana University Paleontology Collections for access to this Diabloceratops cast.
How to Take Photogrammetry Photos for Paleontologists
มุมมอง 1.2K2 ปีที่แล้ว
The key to success with photogrammetry is taking the right photos. Here I go into detail on the lighting and camera set-ups that will produce the best results. Digicam Control: digicamcontrol.com/ Acknowledgements: Special thanks to Adam Rountrey for showing me the set-up at University of Michigan. Thanks to Indiana University Paleontology Collections for access to specimens seen in this video:...
Introduction to Photogrammetry for Paleontologists
มุมมอง 8852 ปีที่แล้ว
Photogrammetry is an incredible technique for turning photographs into 3D scans. Here is a simple explanation of how it works, and comparisons with other 3D methods, so you can know if this is a method that will work for you. Reality Capture: www.capturingreality.com/Meshroom: alicevision.org/#meshroom Acknowledgements: Special thank you to Adam Rountrey (University of Michigan) and Jonathan Ke...
A Day in the Life of a (Virtual) Paleontologist | IU Science Fest 2020
มุมมอง 3373 ปีที่แล้ว
This video covers an abbreviated workflow of scanning and working with scan data of a fossil intended for non-paleontologists. I originally created the video for for Indiana University's Science Fest, an outreach event for the community of Bloomington to see the science happening at IU. For a more in depth explanation of the process used to reconstruct the ulna see this video: th-cam.com/video/...
Putting a Bone Together Workflow | Blender for Paleontologists Video 5
มุมมอง 5883 ปีที่แล้ว
This is my entire workflow for virtually gluing scans of a broken ulna back together in Blender. I left in mistakes and all, so you can see my trouble shooting process as I stitch these scans together. I also show how mirrored elements from the other ulna can be used to fill in some holes. I made this first for figures for an upcoming paper and second for th-cam.com/video/YXGeBOsoBd4/w-d-xo.htm...
Quick Render | Blender for Paleontologists Video 4
มุมมอง 4004 ปีที่แล้ว
Blender comes with many options for materials, lighting, and rendering that can be overwhelming for making a simple figure. In this video, I show my quick settings for making a render of a scan or mesh in Blender for export to a photo editing software like Photoshop. Download Blender: www.blender.org/download/ Morphosource Links: Patriofelis CM 87673 - www.morphosource.org/concern/biological_sp...
Viewport Navigation | Blender for Paleontologists Video 3
มุมมอง 2494 ปีที่แล้ว
This video demonstates how to navigate the Blender viewport using the Industry Compatible Keymap. This includes rotating, panning, and zooming the view, and moving, rotating, and scaling an object. I also show how to quickly center scanned objects. Download the latest version of Blender: www.blender.org/download/ Morphosource Links: www.morphosource.org/concern/biological_specimens/000374168 Ac...
Blender Layout | Blender for Paleontologists Video 2
มุมมอง 4554 ปีที่แล้ว
I go over the layout of Blender and the tools most commonly used by paleontologists. I work with Blender 2.8. If you are interested in more in depth tutorials, I recommend the Blender Guru whose beginner series can be found here: th-cam.com/play/PLjEaoINr3zgEq0u2MzVgAaHEBt xLB6U.html
Introduction | Blender for Paleontologists Video 1
มุมมอง 1.3K4 ปีที่แล้ว
Introduction | Blender for Paleontologists Video 1
Cleaning and Remeshing Filters in Meshlab | Introduction to Digital Preparation Video 16
มุมมอง 54K4 ปีที่แล้ว
Cleaning and Remeshing Filters in Meshlab | Introduction to Digital Preparation Video 16
Selection Tools in Meshlab | Introduction to Digital Preparation Video 15
มุมมอง 9K4 ปีที่แล้ว
Selection Tools in Meshlab | Introduction to Digital Preparation Video 15
Meshlab Interface | Introduction to Digital Preparation Video 14
มุมมอง 8K4 ปีที่แล้ว
Meshlab Interface | Introduction to Digital Preparation Video 14
Mesh Processing Overview | Introduction to Digital Preparation Video 13
มุมมอง 7644 ปีที่แล้ว
Mesh Processing Overview | Introduction to Digital Preparation Video 13
Exporting a Mesh from 3D Slicer | Introduction to Digital Preparation Video 12
มุมมอง 4.4K4 ปีที่แล้ว
Exporting a Mesh from 3D Slicer | Introduction to Digital Preparation Video 12
Segmenting Scans in 3D Slicer | Introduction to Digital Preparation Video 11
มุมมอง 2.9K4 ปีที่แล้ว
Segmenting Scans in 3D Slicer | Introduction to Digital Preparation Video 11
Cropping Volumes in 3D Slicer | Introduction to Digital Preparation Video 10
มุมมอง 8K4 ปีที่แล้ว
Cropping Volumes in 3D Slicer | Introduction to Digital Preparation Video 10
Volume Rendering in 3D Slicer | Introduction to Digital Preparation Video 9
มุมมอง 5K4 ปีที่แล้ว
Volume Rendering in 3D Slicer | Introduction to Digital Preparation Video 9
Navigating 3D Slicer | Introduction to Digital Preparation Video 8
มุมมอง 9764 ปีที่แล้ว
Navigating 3D Slicer | Introduction to Digital Preparation Video 8
Resampling Volumes in 3D Slicer | Introduction to Digital Preparation Video 7
มุมมอง 4.8K4 ปีที่แล้ว
Resampling Volumes in 3D Slicer | Introduction to Digital Preparation Video 7
Converting and Saving an Image Stack in 3D Slicer | Introduction to Digital Preparation Video 6
มุมมอง 4.7K4 ปีที่แล้ว
Converting and Saving an Image Stack in 3D Slicer | Introduction to Digital Preparation Video 6
Importing Data into 3D Slicer | Introduction to Digital Preparation Video 5
มุมมอง 11K4 ปีที่แล้ว
Importing Data into 3D Slicer | Introduction to Digital Preparation Video 5
Overview of CT Scan Volume Processing | Introduction to Digital Preparation Video 4
มุมมอง 5264 ปีที่แล้ว
Overview of CT Scan Volume Processing | Introduction to Digital Preparation Video 4
Types of 3D Data for Virtual Paleontology | Introduction to Digital Preparation Video 3
มุมมอง 6504 ปีที่แล้ว
Types of 3D Data for Virtual Paleontology | Introduction to Digital Preparation Video 3
Hi, thanks a lot for this video. Is there any way to accurately warp to specific configurations of certain specimens on the PCA? The best way I can think of is assuming -100 and 100 on the PC slider correspond to the lowest and highest coordinates of the specimen on those extremes of the PCs and scale the PC slider for each specimen accordingly, which is really tedious and uncertain.
Wow, I had no idea you could Volume Render the preview scan. Great video! You can also drag and drop a scan data folder on top of Slicer and it will prompt you if you want to load it using ImageStacks, it's a minor timesaver but handy. Thanks!!!
Hi @VirtPaleo, awesome tutorial and research! One of the simplest ways to insert a point to a curve is: - have the Markups tool active - hover over the curve so that it gets highlighted (like at the 8:42 timestamp) - Ctrl (Cmd on a Mac) + left click on the curve at the desired location should insert the point there
I tried loading the file and also clicked the single file out so it all comes in. The problem is that the software is not responding every time I want to add on the data, probably because it is huge. Any advice on that?
Increasing the memory of your computer might help.
Is there a way to export the animation of PC warping?
i used obs to record
Quick question re: closed and open curves. Are the points generated when placing an open or closed curve all considered fixed landmarks for curves? Or are they always considered semi landmarks? I was also wondering if I can start and end an open curve using fixed landmarks from the regular control points? That is, I have 14 fixed landmarks on some fossil teeth, and I'd like to add some curves to the already existing coordinate data from my fixed landmarks to better capture the variation I am interested in. Could I used two landmarks from the already established 14 fixed landmarks as the starting control point and the ending control point for an open curve?
Your videos are always very useful, thanks 👍🏻
I'm going to have to watch this several times. Thanks for explaining.
Thank-you for the nice tutorial.
for some reason, it doesnt work with .json files for me :(
Thank you so much, these are incredibly handy for anyone trying to jump into slicer without any prior experience.
would like to know how to make the data set by plotting on my images with in 3-D slicer to create a landmark set for geometric analysis. I understand how to plot the landmarks, but l'm not sure how to export the landmark data per each individual case, to later combine all for geometric analysis as a data set
I usually save the markups as an fcsv and then change the extension to csv if I want just one specimens landmarks
what is the best way to smooth out the spikes created in stl files?
Thank you for this excellent presentation, you have saved me a lot of headaches!
👍Great beginner video. Thanks!
Amazing content!
Mahalo for sharing
Thank you very much
which one is better making maual landmarking or use pseudoLMGenerartor of slicermorph? Please give some advice
My answer is that it greatly depends on your data and there’s a lot of debate about the pros and cons of both. I recommend looking through this paper to get an idea: academic.oup.com/icb/article/59/3/669/5523849
Thank you very much prof@@VirtPaleo. Looks like i've been lost all this time about this morphometric topic and landmarking. Please give me some advice, i'm doing a thesis about human tibial bone statistical shape model, do you think it is ok to just use pseudoLMGenerator then use PCA of slicermorph?
@JOc17KER Any method is going to require some thought and experimentation to capture the variation you're interested and make sure you're seeing actual variation and not mistakes in the data. PseudoLMGenerator would work well for human tibias because there's not a lot of good anatomical landmarks like the skull. I recommend reading Slicermorph's documentation: github.com/SlicerMorph/Tutorials/tree/main/PseudoLMGenerator and paper: besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13669 the later of which has a nice flow chart for how to choose what method will work best for your data.
So to produce the cropped version of yor daraset, you're gonna still need a machine with a lot of ram, Correct?
You shouldn't need as much RAM since the images are being cropped with this method as they're loaded it. I would generally recommend a machine with at least 16GB if you're going to work with Slicer, but that should be pretty easy to get.
@@VirtPaleo 🙏🙏🙏
Hello, I cannot find the data for Volume Information in the .xtekct file which comes with Nikon scans. Do you maybe know what could correspond to Dimension, Spacing, Origin etc.? I have for example voxels and size.
good work!! very nice videos
What an excellent walk through of the plugin!
Wow, this will be super helpful to me and some of my colleagues! The video is very well made, and, except for the analysis part, which I am looking forward to seeing, there is nothing that a new user might miss. Congratulations!
Thanks for this video, it's extremely useful.
Where can I find some sample CT datasets? What is the format that they usually come in? Is it possible to get the voxel data in text format such as: X, Y, Z, R, G, B
I recommend looking on Morphosource: www.morphosource.org/ I have never seen a plain text format for voxel data, but it's possible it's out there.
@@VirtPaleo Thank you - I will check it out! 🙂
Super helpful! Thanks Anne!
Wow! Image Stacks is greatness! Thank you
right on thank you for sharing!!
Hello Sir, I'm having a problem with the mesh data, I can't figure out what tool to use to find the problem. so, I hope you give some suggestion about the tool.
Is there a mirrorless camera good for photogrametry
For loading images, once you've loaded the first image, how to you load the rest to create a volume out of them all?
Loading the first image should load the full stack if 1.) they are all in the same folder in order and 2.) you uncheck the single file option when you add the data (see 2:46). There's another option you can try in the newer version of Slicer as well. Install the SlicerMorph extension and use the ImageStacks module. It lays out all the options pretty clearly for loading in stacks and gives you more options.
Thanks you very muche for your tuto ! I'm trying to segment the ethmoid of a cat but i'm struggling a lot, did you already manage to segment an ethmoid ?
thanks a lot
Hello, thank you for your great video ! I have an issu with the vector to scalar volume, i can't click on the input vector volume, do you know why ?
This is a lifesaver!! Thanks so much for an awesome video!
Thanks for the tutorial! You mentioned using a tablet; presumably, you can't use an iPad for this, no?
I use a Wacom tablet like this: estore.wacom.com/en-US/one-by-wacom-small-ctl472k1a.html I don't think there is anyway to use the iPad, but the lower end wacom tablets are pretty cheap and work just fine.
Hi, thank you for your video tutorials on slicer. Currently i am trying to load a single 16Gb .TIF file into slicer but doesn't load it as a volume, but rather a 4mb 2D image. I know the file works as when i load it on to FIJI it loads as a stack. Do you have any suggestions
Even if it shows up as a single file, you may still have to uncheck single file in the volume options. That would be my best guess but not 100% sure.
I'm so glad I found your channel!
Thank you! A friend just sent me your video testing the portable surface scanner. I can't wait to see what more you do!
Instead of those fake ice cubes you can use transparent plastic caps from rinser bottles, for example. I do this all the time, but I use transparent caps from shaving foam.
Thanks
I'm going to be making a turntable project with Unreal 5 and I think I'm going to use a vinyl turntable to help me. This is a great and very helpful video and I'll share it with my fellow game art students. :)
I've been thinking of writing a script to compare two objects. Say you have scans of two similar bones from two closely related species and you want to visual the similarities and differences. Blender could place both scans at the same location then apply a Boolean difference. The problem is getting the rotations to align. I think it could program a goal seeking algorithm to minimize the volume of the Boolean difference. I have to be careful that the goal seeking does not get caught in an infinite loop. Do you know if anyone has already created something like this?
I use a method called geometric morphometrics. You place landmarks on both objects and have the computer align based on the landmarks. There's a lot of resources on it: Wikipedia is good for a quick intro: en.m.wikipedia.org/wiki/Geometric_morphometrics_in_anthropology Longer course material on it: morphometrics.earth.indiana.edu/#:~:text=P.,David%20Polly&text=Geometric%20Morphometrics%20is%20the%20analysis,curves%2C%20outlines%2C%20or%20surfaces. I use the SlicerMorph extension for Slicer to run everything: slicermorph.github.io/ I'm not sure how well the volume method you describe would work since the minimum volume won't necessarily line up homologous points. I'd be interested to hear how it works if you text it though
hi thank you but i have a problem in loading dcm data. when i import the folder containing some dcm files, it imports all the dcm files seperately as each file correspond to a seperate patient. what should i do please?
Hard for me to say, as it could be a lot of things. My recommendations would be to 1.) Make sure nothing else is in the folder with the DICOM slices, 2.) Make sure you are using the DCM import tool and not the data import tool, and 3.) Check that you have the most recent stable version of Slicer installed (4.11).
I was having an issue with importing my DCM files as well; I tried the DICOM import by selecting all files, normal import by selecting all files, drag-and-drop all selected files at once onto the Volume Rendering window, doing the same with the folder which contained the DCM files, and nothing worked. What ended up working (for me) was the first technique outlined in the video: normal import (for some reason), choose the first file in the series, show options, uncheck "Single File", them load them in. Again, I'm not sure why my DCM files were having trouble importing, and I'm not sure why using the normal, not DICOM, import function ended up working, but it worked for me in my specific situation.
Thank you for this tutorial!
it was very useful, thanks
Cool
Thx a lot, i am forever in your debt
Thanks for tutorial, can you add link to this volume used so I can follow tutorial directly?
Unfortunately I can't share that specific volume since the research on it is still in progress and unpublished. I'd recommend going to morphosource.org and search for some taxa of interest to you!
where i can sell surface scanning ?