Thank you Dr. Buser for the article. I found it very informative and I definitely liked the inclusion of the supplemental videos.
On Monday, August 31, 2020 at 5:23:44 PM UTC-7 [email protected] wrote: > Eric, > > Just adding to Murat's excellent advice here: the quadratic edge collapse > function in Meshlab is very useful for reducing file size of 3D objects. > For my work, I specify a target of 500,000 faces and that gives me a good > balance between not losing too much information in the object, but reducing > the object to a manageable file size for downstream analysis (e.g., reading > into R via geomorph, or the IDAV landmark editor program). > > Some colleagues and I put together a workflow for processing and analyzing > CT data using the programs Fiji and 3D Slicer, both of which are > open-source and cross platform. The workflow is built around working with > CT data, but includes step-by-step instruction for cleaning up and > exporting 3D models in 3D Slicer (Steps 7b, 7c, and 7d), as well as video > tutorials in the supplemental materials that demonstrate 3D model > simplification and file conversion using Meshlab (Supplementary Video S3), > which may be useful in your work. The workflow is available for free from > the open access journal, Integrative Organismal Biology here > <https://academic.oup.com/iob/article/2/1/obaa009/5818881> ( > https://doi.org/10.1093/iob/obaa009). > > I hope that helps and best of luck, > Thaddaeus Buser > > > > On Friday, August 28, 2020 at 8:42:29 PM UTC-7 [email protected] wrote: > >> Eric, >> >> These are all excellent questions to ponder about, particularly when you >> are starting with 3D digitization and morphometrics. Questions you ask >> require validation. The first one, stitching of individual mesh elements to >> form a 3D object, is the hardest one to quantify, because it requires an >> independently acquired image of the same object at a high-resolution >> (preferably with a modality like tomography) so that you can treat that as >> a gold reference. Or you might consider scanning an object of known >> dimensions (e.g., sphere, cube), and then you can compare your results from >> geometric estimates (of volume, area) to the digitized one. From there it >> is somewhat easy to generate heatmaps that will let you visualize the >> difference between your gold-reference and your digitization. Once you >> establish this flow, you can then experiment with your different algorithms >> of stitching and/or data acquisition. >> >> The approach in the second part of the question is the same, but it is >> easier because that point your original mesh would be the reference. Then >> you can experiment with de-noising, smoothing, and remeshing steps and keep >> comparing those to your original mesh to understand the effects of it. I am >> not entirely sure if there is strict order applying the filters, it is more >> about the end result really. I think for stereophotogrammetry steps more >> like fuse, repair, clean. Whether you need remeshing or smoothing (or both) >> will be dependent on your downstream pipeline (e.g., if the tool you are >> using expecting fairly uniformly distributed polygons to create semi >> landmark, you will probably need to remesh). >> >> Again these are all empirical test, and you shouldn't take anybody >> (including mine) as gospel to follow strictly, the idea is to experiment >> and see the results for your particular data. Meshlab is very powerful for >> this, but some of these (particularly some of the clean up tasks) can be >> accomplished fairly easily in 3D Slicer using as well. For a conceptually >> similar exercise on the effect of decimation to mesh geometry you can take >> a look at this tutorial from our recent workshop. >> >> https://github.com/SlicerMorph/S_2020/blob/master/Day_4/Surface_Toolbox/Mesh_edits.md >> >> HTH, >> M >> >> On Friday, August 28, 2020 at 5:27:25 PM UTC-7 [email protected] wrote: >> >>> Hello everyone, >>> >>> I'm just starting out in 3D GM and I'm really stuck when it comes to >>> figuring out a workflow for producing 3D surface meshes that are de-noised >>> without losing topological integrity, making them suitable for analysis. >>> >>> I've been using a NextEngine Ultra HD laser scanner for producing scans. >>> I've then been moving the scans into Meshlab to to do everything else, from >>> aligning and fusing to repairing and smoothing. I've come to view the >>> number of filters in Meshlab to be both a blessing and a curse. I've also >>> looked into MeshMixer, but everything seems to be black-boxed, and that >>> make me a little uneasy. >>> >>> I'm also confused as to the order of steps. Should I fuse my scans and >>> then clean and repair, or vice versa? What is the best way to de-noise? >>> Should I smooth or remesh? In what order should I be applying filters? >>> >>> I'm hoping that someone here might be able to suggest a workflow to >>> guide me through the process or direct me to some publications that can >>> answer all of my questions. Also feel free to suggest some other 3D mesh >>> applications that I'm likely not aware of. >>> >>> Any advice would be greatly appreciated. Thanks everyone! >>> >>> Best, >>> Eric >>> >> -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. 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