Top Tweets for #BigStitcher
Cubic cleared confetti embryonic heart. Imaged with lightsheet @UCSDMicroscopy, processed with #Bigstitcher and visualized with @UCSFChimeraX #FluorescenceFriday
Looking into #BigDataViewer and #BigStitcher to have something nice to show for #FluorescentFriday.
#bioimaging
Happy #FluorescenceFriday! 🎉 Take a look at this Embryonic Confetti mouse heart, beautifully captured using #Zeiss multi-angle lightsheet technology. Processed with #BigStitcher and presented via @UCSFChimeraX. 🐭❤️🔬
@preibischs @luxendo This is great, thanks for sharing the code! We do love #BigDataViewer and are working on better metadata for #BigStitcher.
Our first attempt is already out on our beta release channel, and this will definitely make our life easier to finalize it.
Feedback is very welcome :)
We're playing around with #bigstitcher for the first time with a large ish dataset (~1k 3D tiles, 4 channels) but #bigdataviewer's UI for controlling channels, groups, visibility etc seem to break on these and most elements can't be reached without a scrollbar. Help!
#BigStitcher tutorial by @bc_vellutini, @jogirstmair, @VladimirUlman and @ChriSchmied - we stitched it all #LISH22🔬🖥️🪡💪
Here is the real-time 3D movie acquired as the tongue is licking in real-time. These volumes were then stitched into a contiguous 3D strip, equivalent to a box of histology slides (thanks #BigStitcher!). All contrast is autofluorescence, no added dyes or stains!
Need some guidance on how to process your #lightsheet data with #BigStitcher? Nikita is currently leading further developments of the #mesoSPIM and has provided a short video to help you out #imageprocessing #Fiji #mesoSPIM https://t.co/BGDKmc3Ri4
BTW @preibischs thanks a lot for the video tutorial you placed on YouTube, made my life very easy. Also kudos on the documentation of #BigDataViewer and #BigStitcher
I haven’t played with #BigDataViewer and #BigStitcher for a while. Their new method to change the project to .n5 is awesome 🤩
Also unable to find documentation for how the metadata and XML file should be structured for #N5 in #BigStitcher? It seems the XML file is kept the same, but there is additional metadata necessary for N5?
Starting to play with on-the-fly streaming of our light-sheet data to #N5 for #BigStitcher using Python... has anyone else already tried this? Some progress... but some roadblocks. Would love to learn together!
"BIG DATA II: Registration and Stitching of TB image datasets" video is now available on @NEUBIAS_COST YT channel:
https://t.co/ItA3SbI4uK
@hoerldavid @preibischs @sebastien_tosi @BogovicJohn #NeubiasAcademy #BigStitcher #MosaicExplorerJ #BigWarp @FijiSc @CALM_STP @TheCrick
Today's NeubiasAcademy webinar at 15:30 CET:
BIG DATA II: Registration and Stitching of TB image datasets" with David @hoerldavid , Stephan @preibischs , Sébastien @sebastien_tosi , John @BogovicJohn
Register now: https://t.co/LyxgU4ahyP
@hoerldavid shows off #BigStitcher at #NEUBIASAcademy! @preibischs.
Thanks @NEUBIAS_COST and organizers 💜
@PavelTomancak @guijacquemet @Mnica43402552 @HenriquesLab @preibischs Yes, #bigstitcher can do registrations also for 4D data! Works nicely also for large datasets...
@guijacquemet @Mnica43402552 @HenriquesLab I am not up-to-date but @preibischs had something like that in #SPIMregistration, perhaps now in #bigstitcher. He will tell.
.@cikus3 from @TheCrick giving a very insightful talk about possibilities but also challenges of making lightsheet microscopy attractive to facility users. Also with a shout-out to #BigStitcher for enabling "the journey to the galaxy!"
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