OpenOrganelle

EXPLORE CELLS & TISSUE AT NM RESOLUTION: High res 3D-EM datasets, automated segmentations, & analyses of intracellular sub-structures and organelles

[Aubrey Weigel @avweigel]

Check out the ✨NEW✨ content on OpenOrganelle!
Update includes:
📰A News page
🦠An updated Organelles page
🔍A new backend for dataset metadata which is now stored in a queryable PostgreSQL database

https://t.co/JtDshOV0PL

[Aubrey Weigel @avweigel]

And another gorgeous rendering 🤩 by @philiphubbard : https://t.co/rlCRLlCueV

[Aubrey Weigel @avweigel]

Super cool rendering 😍 by @philiphubbard up on Janelia's YouTube channel: https://t.co/8J7xIpoHF1

[Aubrey Weigel @avweigel]

Ever wanted to learn how to segment organelles in vEM? Or how we (@COSEMdata/@CellMapPT) generate training data for ML efforts? Look no further! You can find it all here in our recent protocol https://t.co/XU366Y4QYy #teamscience #projectteams #openscience

[John Bogovic @BogovicJohn]

Last Friday @CmHulbert presented #Paintera at #I2K2022 . Here, showing some beautiful @COSEMdata on https://t.co/DBh2VXj0kO
https://t.co/bQL3Wccoul
https://t.co/0gUAepFvQa

[OpenOrganelle @OpenOrganelle]

Check out all this amazing data on https://t.co/589YW0frEH!

[Alex Ritter, PhD @AlexRitterPhD]

Honored and humbled that our article was selected for the cover of @ScienceMagazine. The image of the T cell (red) attacking a cancer cell (white) is a digital reconstruction of 3D electron micrographs collected with collaborators @HHMIJanelia. Segmentation/rendering @ariadne_ai

[OpenOrganelle @OpenOrganelle]

@JamesDManton @jtimaging @truenorth_ia Awesome to hear, @JamesDManton ! We’d love to hear more about how you’re using the data. Let us know if there’s anything in particular you are looking for as well and we can try to accommodate!

[AIC at Janelia @AICjanelia]

At long last, the AIC is again accepting proposals! Advance your science with our revolutionary technology and expertise. Deadline is April 15, 2022. Visit https://t.co/4hGHHleWxj to get started. As always, please contact us for technical consultations before submission.

[OpenOrganelle @OpenOrganelle]

Some new updates on the site, including rearranging and cleaning up the dataset pages 🪄.
Also, did you know that you can open (or view) any of the datasets directly in @FijiSc using either File/Import/N5 or Plugins/BigDataViewer/N5 viewer? Check it out!

[Nature Methods @naturemethods]

Research Highlight by @DrArunimaSingh: Researchers from @HHMIJanelia present methods for capturing whole cell EM images. @OpenOrganelle makes these FIB-SEM volumes, reconstructions and models freely available to the public.
https://t.co/cq51xeLQrr

[Assaf Zaritsky @AssafZaritsky]

1:50 pm @avweigel will present EM organelle segmentation @OpenOrganelle (https://t.co/vluSHoV0ts)

2:05 pm Susanne Rafelski will present the latest and the greatest from the @AllenInstitute (https://t.co/yQMpFuheFP)

2/5

[Aubrey Weigel @avweigel]

Come work with us at @HHMIJanelia with the new 🖌 Annotation & Analytics 📊 team https://t.co/ftM18s1OS4. This is a ✨ NEW ✨ multi-disciplinary team that will work with a variety of datasets (1/6)

[OpenOrganelle @OpenOrganelle]

#NewFeature alert! Now you can filter and sort available datasets on https://t.co/AsPswpdvqD. Happy browsing! Thanks @neomorphic and @davisvbennett for the continuous improvements to the site 🌠

[OpenOrganelle @OpenOrganelle]

@JohannesPilic @Andi_Microscopy A lot of these cells were high pressure frozen, then freeze substituted and resin embedded. The process preserved a lot of the cytosolic “stuff” inside the cell, including ribosomes!

[Sadaf Shadan @sshadan]

2 Papers @Nature on the use of enhanced FIB-SEM to image cells and tissues at up to 4nm per voxel. The authors' AI-based analysis pipeline, which they used for reconstruction of 35 organelle classes, is available via OpenOrganelle
https://t.co/R45XV88XGw

https://t.co/NOONrgXYbL

[OpenOrganelle @OpenOrganelle]

We’ve also gotten a facelift! 💁‍♀️ Browse all the related data for these papers and more - AND - volume renderings are now available for most segmentations. Check it out on https://t.co/2sHzCyO5zC !

[Aubrey Weigel @avweigel]

It’s official! Our manuscript is out today in @Nature. 🥳 Additions since our preprint include a comparison of generalists trained on all training data vs specialists trained on subsets (spoiler alert: generalists win!) and #moreGolgi!
https://t.co/JK2WFMWvmM (1/3)

[OpenOrganelle @OpenOrganelle]

Sounds like a great course!

[Assaf Zaritsky @AssafZaritsky]

Final session of @bengurionu data science in cell imaging course!

Course summary and @OpenCellCZB, @OpenOrganelle, and @AllenInstitute public resources

Slides are up https://t.co/O5jTJ7HMJb, ping me for recordings!

Still curious to see how students' projects will turn out :-)

[OpenOrganelle @OpenOrganelle]

You can explore the all FIB-SEM data published here on https://t.co/l3i4qbez4n!

[Lippincott-Schwartz Lab @JLS_Lab]

Excited to share our work on ER-to-Golgi trafficking and the dynamic nano-anatomy of ER exit sites in mammalian cells! @chiluncellbio @avweigel (1/4) https://t.co/n96Rr7G9jX

[Real Scientists DE @realsci_DE]

Ein phänomenales Mikroskopie-Projekt (von @HHMIJanelia) veröffentlicht ganze Elektronenmikroskopische Datensätze von unterschiedlichen Zelltypen um die einzelnen Zellbestandteile zu visualisieren: https://t.co/LEDsPpQMt5 @OpenOrganelle

[Krishna Mudumbi @KrishnaMudumbi]

Looks like I'll be spending a lot of time playing around with https://t.co/miQ8529h57 soon!

Great talk from @avweigel with such beautiful pictures (as always) at #AIM2021