#volumeem — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #volumeem, aggregated by home.social.
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@innuendo @jernej__s @ZachWeinersmith
Our eFIB-SEM (as per Xu et al. 2017 https://elifesciences.org/articles/25916 ) runs 24/7 for up to 8 weeks, when it runs out of source. And it's essential that it does so, uninterrupted, since it's imaging at nanometre resolution, milling 2 nm slices at a time with an ion beam and then repeatedly imaging the block face. The process is unsurprisingly very sensitive; was hard enough to overcome the reheat cycle of the instrument itself (every 60 hours or so) by detecting it, de-engaging the beams and then seamlessly re-engaging with the block face.
A brief video of the kind of data we acquire:
https://youtu.be/p4MH4-I-P5IThe MS Windows computer deciding to reboot on its own is unacceptable.
#ElectronMicroscopy #Zeiss #FIBSEM #VolumeEM #vEM #Drosophila
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@innuendo @jernej__s @ZachWeinersmith
Our eFIB-SEM (as per Xu et al. 2017 https://elifesciences.org/articles/25916 ) runs 24/7 for up to 8 weeks, when it runs out of source. And it's essential that it does so, uninterrupted, since it's imaging at nanometre resolution, milling 2 nm slices at a time with an ion beam and then repeatedly imaging the block face. The process is unsurprisingly very sensitive; was hard enough to overcome the reheat cycle of the instrument itself (every 60 hours or so) by detecting it, de-engaging the beams and then seamlessly re-engaging with the block face.
A brief video of the kind of data we acquire:
https://youtu.be/p4MH4-I-P5IThe MS Windows computer deciding to reboot on its own is unacceptable.
#ElectronMicroscopy #Zeiss #FIBSEM #VolumeEM #vEM #Drosophila
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@innuendo @jernej__s @ZachWeinersmith
Our eFIB-SEM (as per Xu et al. 2017 https://elifesciences.org/articles/25916 ) runs 24/7 for up to 8 weeks, when it runs out of source. And it's essential that it does so, uninterrupted, since it's imaging at nanometre resolution, milling 2 nm slices at a time with an ion beam and then repeatedly imaging the block face. The process is unsurprisingly very sensitive; was hard enough to overcome the reheat cycle of the instrument itself (every 60 hours or so) by detecting it, de-engaging the beams and then seamlessly re-engaging with the block face.
A brief video of the kind of data we acquire:
https://youtu.be/p4MH4-I-P5IThe MS Windows computer deciding to reboot on its own is unacceptable.
#ElectronMicroscopy #Zeiss #FIBSEM #VolumeEM #vEM #Drosophila
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@innuendo @jernej__s @ZachWeinersmith
Our eFIB-SEM (as per Xu et al. 2017 https://elifesciences.org/articles/25916 ) runs 24/7 for up to 8 weeks, when it runs out of source. And it's essential that it does so, uninterrupted, since it's imaging at nanometre resolution, milling 2 nm slices at a time with an ion beam and then repeatedly imaging the block face. The process is unsurprisingly very sensitive; was hard enough to overcome the reheat cycle of the instrument itself (every 60 hours or so) by detecting it, de-engaging the beams and then seamlessly re-engaging with the block face.
A brief video of the kind of data we acquire:
https://youtu.be/p4MH4-I-P5IThe MS Windows computer deciding to reboot on its own is unacceptable.
#ElectronMicroscopy #Zeiss #FIBSEM #VolumeEM #vEM #Drosophila
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@innuendo @jernej__s @ZachWeinersmith
Our eFIB-SEM (as per Xu et al. 2017 https://elifesciences.org/articles/25916 ) runs 24/7 for up to 8 weeks, when it runs out of source. And it's essential that it does so, uninterrupted, since it's imaging at nanometre resolution, milling 2 nm slices at a time with an ion beam and then repeatedly imaging the block face. The process is unsurprisingly very sensitive; was hard enough to overcome the reheat cycle of the instrument itself (every 60 hours or so) by detecting it, de-engaging the beams and then seamlessly re-engaging with the block face.
A brief video of the kind of data we acquire:
https://youtu.be/p4MH4-I-P5IThe MS Windows computer deciding to reboot on its own is unacceptable.
#ElectronMicroscopy #Zeiss #FIBSEM #VolumeEM #vEM #Drosophila
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"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).
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"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).
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"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).
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"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).
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"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).
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Zurich Winter School 2026 on electron microscopy techniques, run by Dr. Miriam Lucas and colleagues.
Dates: January 19-23rd, 2026
Apply by November 17th, 2025.
"A hands-on, week-long course for PhD students, postdocs, and microscopy enthusiasts eager to deepen their expertise in cutting-edge microscopy techniques."
🎯 Practical modules on Advanced and Super-Resolution LM, Sample Preparation for EM, CLEM, and volume EM
https://scopem.ethz.ch/education/schools/WinterSchool2026.html
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Zurich Winter School 2026 on electron microscopy techniques, run by Dr. Miriam Lucas and colleagues.
Dates: January 19-23rd, 2026
Apply by November 17th, 2025.
"A hands-on, week-long course for PhD students, postdocs, and microscopy enthusiasts eager to deepen their expertise in cutting-edge microscopy techniques."
🎯 Practical modules on Advanced and Super-Resolution LM, Sample Preparation for EM, CLEM, and volume EM
https://scopem.ethz.ch/education/schools/WinterSchool2026.html
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From Elizabeth Marin at Zoology Dept., Cambridge University:
"Together with Greg Jefferis (MRC LMB, Cambridge), Wei-Chung Allen Lee (Harvard Medical School), and Meg Younger (Boston University), I have secured a £4.8M Wellcome Discovery Award to generate a mosquito brain connectome and investigate chemosensory circuits involved in human host-seeking."
"We are currently recruiting for two research assistant positions based in the Zoology department at Cambridge University. Please share this post with any likely candidates :)."
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"Comparative connectomics of Drosophila descending and ascending neurons", Tomke Stürner et al. 2025 (Greg Jefferis and Katharina Eichler's labs).
https://www.nature.com/articles/s41586-025-08925-zCompares between males and females.
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GridTape TEM with beam deflection to reduce stage movements and increase imaging throughput:
"Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy", Zhao et al. 2024
https://www.nature.com/articles/s41467-024-50846-4
#TEM #GridTapeTEM #vEM #VolumeEM #connectomics #neuroscience #microscopy #ElectronMicroscopy
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Thanks for sharing this – will have to think about it. In our case, we built in-house the gridtape reel holders which amount to a custom stage with a mini-camera in it for identifying slots and controlling imaging. So we don't use the factory-supplied stage.
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True as always that the way to make software run faster is to make it do less operations. After all, CPUs can only execute a fixed number of operations per unit of time.
Here, I tweaked code for serial section registration that drops execution time from 27 seconds to 100 milliseconds: a 270x speed up.
All it had to do is to search for matching SIFT features in one image only within a predetermined radius centered on one SIFT feature in another image. Extremely effective for when e.g., the maximum translation is known.
The matching code using a KDTree:
https://github.com/acardona/scripts/blob/master/java/asm/my/PointMatchesFast.java#L56The test script:
https://github.com/acardona/scripts/blob/dev/python/imagej/FIBSEM/tests/test_matchNearbyFeatures.py -
From Moritz Helmstaedter on #RoboEM:
"In today’s AI research, any project lasting longer than 6 months is considered slow, if not outdated and overrun by history. RoboEM, with a concept and an approach that seem quite plausible, still took 5 years from idea to the fully evaluated tool reported here. This was only possible with the patient support of the Max Planck Society, which encourages long-term projects, and the tenacity of the first author. Details made all the difference. And, as often, dead ends had to be avoided efficiently. We had to abandon, for example, the idea of using steering variability to indicate branch points — a nice analogy to road intersections in car steering, but too far-fetched to work well enough in brain tissue data. Sometimes giving up beloved ideas is as important as following through on others. M.H."
#connectomics #volumeEM #vEM #neuroscience #MaxPlanckSociety
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We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures
https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1
All the analyses, plots and figures should be reproducible in #rstats with the code provided:
https://zenodo.org/doi/10.5281/zenodo.10825370
by querying our public #CATMAID database:
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We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures
https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1
All the analyses, plots and figures should be reproducible in #rstats with the code provided:
https://zenodo.org/doi/10.5281/zenodo.10825370
by querying our public #CATMAID database:
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We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures
https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1
All the analyses, plots and figures should be reproducible in #rstats with the code provided:
https://zenodo.org/doi/10.5281/zenodo.10825370
by querying our public #CATMAID database:
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We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures
https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1
All the analyses, plots and figures should be reproducible in #rstats with the code provided:
https://zenodo.org/doi/10.5281/zenodo.10825370
by querying our public #CATMAID database:
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We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures
https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1
All the analyses, plots and figures should be reproducible in #rstats with the code provided:
https://zenodo.org/doi/10.5281/zenodo.10825370
by querying our public #CATMAID database:
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“Perception: How larvae feel the world around them” by Jimena Berni https://elifesciences.org/articles/96708
… an insight piece on Andreas Thum’s lab work on mapping the sensory organs of the #Drosophila larva with electron microscopy:
“Morphology and ultrastructure of external sense organs of Drosophila larvae”
Richter et al. 2024 https://elifesciences.org/articles/96708 -
Christel Genoud is recruiting an electron microscopy specialist at the University of Lausanne:
https://wp.unil.ch/emf/?trk=feed-detail_main-feed-card-text -
EM stack of a golgi ribbon in a glial cell of #Platynereis, from Benvenuto et al.,:
"Evolution of the ribbon-like organization of the Golgi apparatus"
with small contribution from our lab.
https://www.sciencedirect.com/science/article/pii/S2211124724001190?via%3Dihub
#CellBiology #volumeEM #cell -
Our new EU PhD Network #ZooCell is hiring! We have 12 PhD positions in Germany, France, UK, Italy and Sweden.
The broad topic is evolution of sensory cell types in animal diversity: multidisciplinary training in 3D cellular reconstruction (volume EM), multimodal data analysis and science outreach.
https://euraxess.ec.europa.eu/jobs/189511
Please share!
If you are interested in a PhD in #volumeEM, comparative #connectomics etc. check out the projects and apply!
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Positions available at the Human Technolopole in Milan, Italy:
* Bioimage Analyst https://careers.humantechnopole.it/o/bioimage-analyst
* Research Software Engineer https://careers.humantechnopole.it/o/software-engineers
CC @florianjug
#python #java #volumeEM #ElectronMicroscopy #Relion #IMOD #CryoEM #Fedihire
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A connectome of the optic lobe of the extremely tiny fairy wasp, Megaphragma sp.
"A complete reconstruction of the early visual system of an adult insect", by Chua et al. 2023 (Chklovskii & Polilov) https://www.sciencedirect.com/science/article/pii/S096098222301237X
Don't miss the supplemental figures.
"Compared with the honeybee and the fruit fly, Megaphragma exhibits the following miniaturization-related adaptations: a significant reduction in the number of ommatidia, absence of several cell types, reduced size, and denucleation of neurons. Interestingly, the reduction in lens diameter is less than that expected from the optimization of the optical resolution of the eye. This suggests that light sensitivity is a more important
consideration when lens diameter approaches the wavelength of light. The absence of wide-field (or non-columnar) lamina neurons in Megaphragma could be a consequence of the smaller number of ommatidia, their larger acceptance angle, and the lower resolving power of the eye."Volume assembled with #FijiSc and #TrakEM2, and its neurons and synapses mapped with #CATMAID. Woohoo!
#neuroscience #connectomics #VolumeEM #vEM #insects #miniaturization
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Unprecedented nanometer-scale structures of cristae in >400 individual #mitochondria, by @Hirabayashi_Lab, using a novel deep learning-based analysis of #volumeEM images, (also reveals previously unknown function of OPA1) #PLOSBiology https://plos.io/3OXtPzK
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Following from Collinson's paper, here is my take on scaling up volume electron microscopy for connectomics in the #UK or any country willing to commit about 10 to 20 million a year:
"Growing and nurturing a research base in connectomics"
https://albert.rierol.net/tell/20230823_connectomics_research_base.htmlFrom the humble #Drosophila to the #mouse brain, passing through the mosquito, honeybee, gecko lizards and the Etruscan shrew.
It's possible, it's feasible, it's timely: therefore we must.
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"Volume EM: a quiet revolution takes shape" – a review and commentary by Lucy Collinson et al. 2023 on present and future electron microscopy technology and its application https://www.nature.com/articles/s41592-023-01861-8
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Amusing that the piece includes optical microscopy methods unrelated to neural function, such as STED, PALM, expansion microscopy and CLARITY, but ignores electron microscopy methods key to the current boom in #connectomics. In particular, Denk and Horstmann 2004 for SBEM https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020329 , Knott et al. 2008 for first application of FIBSEM to neuronal tissue https://www.jneurosci.org/content/28/12/2959 , Schalek et al. 2011 for the ATUM serial section tape-collecting system https://academic.oup.com/mam/article-abstract/17/S2/966/6947317 , Xu et al. 2017 for e-FIBSEM and Graham et al. 2019 for GridTape TEM https://www.biorxiv.org/content/10.1101/657346.abstract
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For any #3DEM #volumeEM people: is there an alternative software for skinning that you can recommend?
I’m building a 3D model of a complex subcellular structure, using 3DMOD. During skinning, imodmesh is generating a many misconnections. I've minimised them but I’m wondering if other software has better algorithms for generating the mesh.
FOSS-preferred. Please don't suggest Amira!
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For any #3DEM #volumeEM people: is there an alternative software for skinning that you can recommend?
I’m building a 3D model of a complex subcellular structure, using 3DMOD. During skinning, imodmesh is generating a many misconnections. I've minimised them but I’m wondering if other software has better algorithms for generating the mesh.
FOSS-preferred. Please don't suggest Amira!
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For any #3DEM #volumeEM people: is there an alternative software for skinning that you can recommend?
I’m building a 3D model of a complex subcellular structure, using 3DMOD. During skinning, imodmesh is generating a many misconnections. I've minimised them but I’m wondering if other software has better algorithms for generating the mesh.
FOSS-preferred. Please don't suggest Amira!
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For any #3DEM #volumeEM people: is there an alternative software for skinning that you can recommend?
I’m building a 3D model of a complex subcellular structure, using 3DMOD. During skinning, imodmesh is generating a many misconnections. I've minimised them but I’m wondering if other software has better algorithms for generating the mesh.
FOSS-preferred. Please don't suggest Amira!
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For any #3DEM #volumeEM people: is there an alternative software for skinning that you can recommend?
I’m building a 3D model of a complex subcellular structure, using 3DMOD. During skinning, imodmesh is generating a many misconnections. I've minimised them but I’m wondering if other software has better algorithms for generating the mesh.
FOSS-preferred. Please don't suggest Amira!
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Hot off the presses! 📖🔬📣
@[email protected]'s #OMEZarr drawings are now in print. Very timely for the first #volumeEM #GordonConf. ❤️
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And it begins... the 1st #GordonConf on #volumeEM!
Thanks for the invitation to #vEMtura23 🤩🌅🔬🧊
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"Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation", by Marin et al. 2023 (Greg Jefferis lab at #MRCLMB in collaboration with #HHMIJanelia and others).
https://www.biorxiv.org/content/10.1101/2023.06.05.543407v1
On the analysis of the #Drosophila male adult nerve cord (#MANC), reconstructed from #VolumeEM by Takemura et al. 2023 (preprint still pending to come out).
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"Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation", by Marin et al. 2023 (Greg Jefferis lab at #MRCLMB in collaboration with #HHMIJanelia and others).
https://www.biorxiv.org/content/10.1101/2023.06.05.543407v1
On the analysis of the #Drosophila male adult nerve cord (#MANC), reconstructed from #VolumeEM by Takemura et al. 2023 (preprint still pending to come out).
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"Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation", by Marin et al. 2023 (Greg Jefferis lab at #MRCLMB in collaboration with #HHMIJanelia and others).
https://www.biorxiv.org/content/10.1101/2023.06.05.543407v1
On the analysis of the #Drosophila male adult nerve cord (#MANC), reconstructed from #VolumeEM by Takemura et al. 2023 (preprint still pending to come out).
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"Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation", by Marin et al. 2023 (Greg Jefferis lab at #MRCLMB in collaboration with #HHMIJanelia and others).
https://www.biorxiv.org/content/10.1101/2023.06.05.543407v1
On the analysis of the #Drosophila male adult nerve cord (#MANC), reconstructed from #VolumeEM by Takemura et al. 2023 (preprint still pending to come out).
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"Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation", by Marin et al. 2023 (Greg Jefferis lab at #MRCLMB in collaboration with #HHMIJanelia and others).
https://www.biorxiv.org/content/10.1101/2023.06.05.543407v1
On the analysis of the #Drosophila male adult nerve cord (#MANC), reconstructed from #VolumeEM by Takemura et al. 2023 (preprint still pending to come out).
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Doncs ...
#BigStitcher https://www.nature.com/articles/s41592-019-0501-0
#BigDataViewer https://www.nature.com/articles/nmeth.3392
#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540
#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794
Elastic volume registration https://www.nature.com/articles/nmeth.2072
#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3
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Doncs ...
#BigStitcher https://www.nature.com/articles/s41592-019-0501-0
#BigDataViewer https://www.nature.com/articles/nmeth.3392
#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540
#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794
Elastic volume registration https://www.nature.com/articles/nmeth.2072
#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3
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Doncs ...
#BigStitcher https://www.nature.com/articles/s41592-019-0501-0
#BigDataViewer https://www.nature.com/articles/nmeth.3392
#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540
#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794
Elastic volume registration https://www.nature.com/articles/nmeth.2072
#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3
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Doncs ...
#BigStitcher https://www.nature.com/articles/s41592-019-0501-0
#BigDataViewer https://www.nature.com/articles/nmeth.3392
#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540
#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794
Elastic volume registration https://www.nature.com/articles/nmeth.2072
#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3