Stephan Preibisch @preibischs@qoto.org
Open Science Software Enthusiast - Director of Scientific Computing Software & Team Leader Computational Method Development at HHMI Janelia
Joined Nov 2022
Stephan Preibisch
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Thanks to @konrad_rokicki, @neomorphic, and the rest of the NeuronBridge team. For more details, see:
Volume rendering: https://github.com/JaneliaSciComp/web-vol-viewer
NeuronBridge: https://doi.org/10.1101/2022.07.20.500311
Color depth search: https://doi.org/10.1101/318006
FlyLight Split-GAL4: https://doi.org/10.7554/eLife.43079
FlyEm Hemibrain: https://doi.org/10.7554/eLife.57443
(5/5)
Stephan Preibisch
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Twitter– gehen oder bleiben? Und ist Mastodon eine echte Alternative? Die Plattform wissenschaftskommunikation.de hat sich dem Thema genähert und #Wisskomm-Profis zu Wort kommen lassen. Mit dabei ist auch Anne Rother von der FZJ-Unternehmenskommunikation: https://www.wissenschaftskommunikation.de/twitter-gehen-oder-bleiben-63465/
Stephan Preibisch
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I'm a Software Engineer at @HHMI 's #Janelia Research Campus in Scientific Computing. Where I work on software related to microscopy where I mostly use #JuliaLang, #Java, and #Python. I'm interested in Open Science, Open Data, and Open Source Software.
I was formerly a postdoc in Cell Biology at #Northwestern and #UTSouthwestern and a graduate student in Systems Biology and Biophysics at #UTSW and #UCSD. I concentrated in Biological Chemistry and Mathematics at #UChicago.
@Volker But a zipped test project would be great to have! Thanks so much :)
Stephan Preibisch
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Here's the proper announcement, please spread far and wide! Come to our lab for this 2-year funded position, and get our SMLM imaging and analysis to the next level. Please check the details below, read the full ad on our website, and contact me for more https://neurocytolab.org/positions-2/
@Volker Hi, you can simply run it on your local computer where you define the number of threads Spark can use (e.g. -Dspark.master=local[8]). Running it on a cluster or cloud requires more setup. But I'll also try to add these optimizations to BigStitcher directly!
@Volker Actually, I have not tried this on 2D data, only 3D ... there might be a few bugs in there for the 2D case still.
@Volker That is fixed when you use BigStitcher-Spark: https://github.com/PreibischLab/BigStitcher-Spark/blob/main/README.md
It supports affine and non-rigid fusion to N5, ZARR, HDF5 (HDF5 only when running locally on a computer). It can even run in a cluster & cloud environment.
Happy to help with it!
@kapalpecah that worked, thanks a lot, very confusing though.
@albertcardona yeah, typing the full qoto.org worked, very confusing though ... thanks a lot!
Does anyone know why the Apple mastodon app doesn’t know #qoto ?
This is a very useful webpage if you would like to contact any company about any issue:
Stephan Preibisch
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We have an exceptional opportunity at our center for a new group leader at VIB in Leuven. We are looking for a new colleague who wants to use computational methods to investigate molecular and/or cellular aspects of neurobiology. This position not only comes with substantial and renewable core funding and start-up package, but it is also linked to a tenure track position at KU Leuven.
More information on our center can be found on our website https://cbd.sites.vib.be/en.
Just fixed a major bug (forgot to upload a new version of imglib2-algorithm to the Fiji update site) ... now it works properly
Stephan Preibisch
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Neuro-evo conference at HHMI Janelia on May 15-18, 2023. Join us for the third edition!
Application deadline: Jan 27 (11:59 p.m. EST) 2023.
"Historically, with the study of the most convenient animal models —from the giant axon of the squid and the lobster's stomatogastric circuits to Aplysia's synapses and C. elegans' circuits — neuroscientists revealed some of the operating principles of the nervous system, which were then found to apply broadly across phyla. The third instalment of this meeting will once again bring together neuroscientists working on a broad diversity of animal models in an effort to compare circuits across phyla as a means to crack their function."
#NeuroEvo #Janelia #HHMI #conference #science #academia #neuroscience #DevBio #connectomics #connectome
Stephan Preibisch
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Cap-dependent #translation initiation monitored in living cells: https://rdcu.be/cYNJ6.
Collaborative science during a pandemic ❤️
#OpenAccess #TranslationalControl #InitiationFactors #ParticleTracking
@preibischs
Unbelievable, multiview-reconstruction & BigStitcher have finally lost their Imglib1-dependency! And all processing is now virtual thus scaling to larger volumes ... @herrsaalfeld
https://github.com/preibischlab/multiview-reconstruction
https://github.com/PreibischLab/BigStitcher
I really like that the complete peer review is now available for everyone to look at: https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-022-01669-y/MediaObjects/41592_2022_1669_MOESM3_ESM.pdf
RS-FISH was just released as open access article in @naturemethods RS-FISH is a user-friendly software for accurate spot detection that is applica...
@herrsaalfeld @naturemethods @davi
* yes, 4,072 peta-pixels is ~4 exa-pixels - I just thought people can relate more to peta than exa.
* I did not know that 2^63 blocks are supported ... that increases that number significantly ... mmh
RS-FISH was just released as open access article in @naturemethods
RS-FISH is a user-friendly software for accurate spot detection that is applicable to smFISH experiments, spatial transcriptomics, and spatial genomics. The approach enables fast spot detection in even very large volumetric datasets.
https://github.com/PreibischLab/RS-FISH
https://github.com/PreibischLab/RS-FISH-Spark
Open Science Software Enthusiast - Director of Scientific Computing Software & Team Leader Computational Method Development at HHMI Janelia
Joined Nov 2022
