scalable minds

We build tools and services for large-scale neuroscience. @webknossos

[Norman Rzepka 🇺🇦 @normanrz]

Storing, sharing, visualizing and processing large #volumeEM data can be challenging. Selecting the right file format is the basis for making things easier.
Our article „Toward scalable reuse of vEM data: OME-Zarr to the rescue“ is out now: https://t.co/GnVpr8dy7I 🧵1/5

[Norman Rzepka 🇺🇦 @normanrz]

Major publication by our friends at @mh_lab @MpiBrain! We used our Voxelytics software to help with fully automatic neuron segmentation, synapse detection, and connectome generation for 9 EM datasets from Mouse, Macaque, and Human.
All datasets are available at @webknossos.

[Jonathan Striebel @jostriebel]

@PyConDE was awsome! Big thanks to all the amazing organisers, volunteers & speakers! #PyConDE #PyDataBerlin

[Jonathan Striebel @jostriebel]

Going to present speedup steps that made data analysis code 700% faster, today at 2PM, #PyConDE
https://t.co/Iri7EBDuka

Big thanks to my amazing colleagues at @scalableminds for the help and feedback preparing it 🙏

[WEBKNOSSOS @webknossos]

Find a soma, select the skeleton annotation tool, move between the slices of your data and place nodes until your neurite ends... Learn everything about skeleton annotations in webKnossos in @tom_herold 's blog post!

https://t.co/ZW9b9qC1M6

#Connectome #BioImageAnalysis

[David A. Markowitz @DavidAMarkowitz]

There are now (at least) 4 companies offering neural circuit reconstruction as a service: Zetta AI, Ariadne AI, Scalable Minds, and Unidesign Solutions. I think all require you to bring your own EM data, but I'm sure we'll see sample prep and image acquisition as a service soon.

[WEBKNOSSOS @webknossos]

Read our blogpost about Machine learning workflows for large-scale reconstruction projects and discover how to make the most out of webKnossos for such use cases!
https://t.co/W6CMWQpTGC
#MachineLearning #Connectome

[WEBKNOSSOS @webknossos]

Do you need ground truth for your deep learning project? Check out our manual annotation service. Get high-quality annotations from our trained annotators for your image data. Learn more: https://t.co/5MYBEfzEZj

[WEBKNOSSOS @webknossos]

Read @normanrz 's blogpost to learn everything you need about meshes in webKnossos!

https://t.co/ZzsHTrEHho

[WEBKNOSSOS @webknossos]

Render your meshes with your favorite tool. Choose a loaded mesh in the "Meshes" tab, then download it in STL. Import it into your rendering software (such as Blender or Amira) and let your graphic skills shine!

Read more: https://t.co/StZ07wURmF

[WEBKNOSSOS @webknossos]

webKnossos now supports precomputed meshes. Click on a segment and instantly view the object in 3D. Try a demo: https://t.co/RnAifaCS2V

[WEBKNOSSOS @webknossos]

We're introducing a dark mode to webKnossos! 🌙
Take it easy on your eyes when working those late hours or in dark environments or simply enjoy its aesthetic.

[WEBKNOSSOS @webknossos]

webKnossos now supports multisection tiffs and image sequences on upload. 🎉
Let us know what formats we should add next!

[WEBKNOSSOS @webknossos]

Read about new annotation and usability features in webKnossos in our latest blog post!
https://t.co/EgvHgx1iDa

[WEBKNOSSOS @webknossos]

https://t.co/0wSoQOYz1l now features a site listing publications which used webKnossos in their work. Please contact us if we missed your publication!
https://t.co/ilrpTKOJgs

[WEBKNOSSOS @webknossos]

We're introducing a pilot program for webKnossos. Receive up to 10TB of storage for free and help us shape the future of webKnossos.
Apply now at https://t.co/LDWNVs9pW6

[Anjali Gour @AnjaliGour18]

@webknossos @ScienceMagazine @boergens @mh_lab Big thanks to the super amazing team at @scalableminds for their help and support! :)

[WEBKNOSSOS @webknossos]

New publication with 10 novel datasets available on https://t.co/0wSoQOYz1l: "Postnatal connectomic development of inhibition in mouse barrel cortex"
Published in @ScienceMagazine by @AnjaliGour18, @boergens, N Heike, Y Hua, P Laserstein, K Song, @mh_lab

[WEBKNOSSOS @webknossos]

New publication data on https://t.co/0wSoQOYz1l: "Electron Microscopic Reconstruction of Neural Circuitry in the Cochlea" (Cell Reports) by Hua et al.
Published at @CellReports!
Check it out now: https://t.co/u0HxSbUuIz

[Moritz Helmstaedter @mh_lab]

@albertcardona @dddavi @bpedigod @DanBumbarger @KordingLab @AdamMarblestone @TonyZador @bdanubius @neuro_data @ylecun @darbly @csdashm @marccobe @stardazed0 @blamlab @criticalneuro @as_bates @gsxej @alfairhall @JustusKebschull @catmaid We are hosting many datasets on https://t.co/YeyidN2QRD openly available - can browse on most mobile phones. Eg https://t.co/j0BR7LohlG #webknossos @scalableminds