COSEM

Using machine learning and computer vision techniques to automatically identify and quantify all intracellular substructures & organelles in isotropic EM data

[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]

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!

[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)

[COSEM @COSEMdata]

Check out the new feature on https://t.co/wVhX9vTczj!

[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 🌠

[Marius Pachitariu @marius10p]

Still hiring for these positions at Janelia!

[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

[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]

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 !

[OpenOrganelle @OpenOrganelle]

Sounds like a great course!

[COSEM @COSEMdata]

😍

[Michael Morehead @michael_syglass]

@romainGuiet @fabrice_senger @waisman_ar @Gonza_Saba @uschmidt83 @jytinevez @FijiSc You might also consider using the free version of syGlass. https://t.co/SUSZzGkqHx

It's significantly better with a VR headset, but the rendering is so choice. [Data credit to @COSEMdata ]

[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

[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

[Ulrike Boehm 🔬👩🏻‍💻 @Ulrike_Boehm]

Meet Aubrey Weigel! @avweigel leads the @COSEMdata Team at @HHMIJanelia which is developing ML approaches to automatically identify & quantify all intracellular structures in FIB-SEM datasets of mammalian cells 🔬👩🏻‍💻 Happy #WomenScienceDay! #womenatjanelia #womeninscience 3/4

[Ulrike Boehm 🔬👩🏻‍💻 @Ulrike_Boehm]

Meet Lorena Benedetti!@LorenaBenedet15 is a postdoc in the Ryan & @jls_lab at @HHMIJanelia. She studies the role of the endoplasmic reticulum at the nerve terminal 🧫🔬👩🏻‍💻 Happy #WomenScienceDay! #womenatjanelia #womeninscience 2/4

[Ulrike Boehm 🔬👩🏻‍💻 @Ulrike_Boehm]

Meet Helen Farrants! @HelenFarrants is a postdoc in the @ERSchreiter lab at @HHMIJanelia. She is developing bright #biosensors for imaging neuronal activity in living organisms 🧪🌈🧑🏼‍🔬 Happy #WomenScienceDay! #womenatjanelia #womeninscience 1/4

[Luciano Lucas @lucianoaglucas]

Check out @COSEMdata and https://t.co/GLajxN5RKY

[Luciano Lucas @lucianoaglucas]

Amazing presentation at #AIMicroscopy Symposium: "Automatic whole cell organelle segmentation in volumetric electron microscopy" @avweigel

@HHMIJanelia @BogovicJohn @herrsaalfeld @herrsaalfeld et al.

https://t.co/167ItMn1Ym

#Unet #deeplearning #microscopy

[COSEM @COSEMdata]

This is dope!

[Michael Morehead @michael_syglass]

what if you could explore biology in 3D, utilizing real data from microscopes? what if experts could easily create compelling VR experiences with their own data?

new version of @syGlassVR dropping in February 🔬

[COSEM @COSEMdata]

Thanks for the lovely write up @mariana_deniz in @preLights summarizing our recent preprint! https://t.co/qmGIKc0TGg