Using machine learning and computer vision techniques to automatically identify and quantify all intracellular substructures & organelles in isotropic EM data
Joined November 2020
- Tweets 24
- Following 97
- Followers 146
- Likes 91
1 Photos and videos
COSEM retweeted
5 Oct 2022
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 protocols.io/view/amira-anno⦠#teamscience #projectteams #openscience
ALT organelle segmentation
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COSEM retweeted
10 May 2022
Last Friday @CmHulbert presented #Paintera at #I2K2022 . Here, showing some beautiful @COSEMdata on openorganelle.org/
youtube.com/watch?v=rNJotgwUβ¦
github.com/saalfeldlab/paintβ¦
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COSEM retweeted
14 Feb 2022
Some new updates on the site, including rearranging and cleaning up the dataset pages πͺ.
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!
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COSEM retweeted
2 Nov 2021
Come work with us at @HHMIJanelia with the new π Annotation & Analytics π team tinyurl.com/5xxy2v95. This is a β¨ NEW β¨ multi-disciplinary team that will work with a variety of datasets (1/6)
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21 Oct 2021
Check out the new feature on OpenOrganelle.janelia.org!
21 Oct 2021
#NewFeature alert! Now you can filter and sort available datasets on OpenOrganelle.janelia.org. Happy browsing! Thanks @neomorphic and @davisvbennett for the continuous improvements to the site π
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COSEM retweeted
7 Oct 2021
Still hiring for these positions at Janelia!
7 Aug 2020
We are looking for postdocs to do cool stuff with our upgraded mesoscope @HHMIJanelia. Now up to 50,000 neurons recorded simultaneously @ 3Hz in two planes. Full ad here: janelia.org/lab/pachitariu-lβ¦
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COSEM retweeted
6 Oct 2021
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
go.nature.com/3lhin4w
go.nature.com/3oEsthG
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COSEM retweeted
6 Oct 2021
Itβs official! Our manuscript is out today in @Nature. π₯³ 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!
rdcu.be/cy1UJ (1/3)
17 Nov 2020
We are proud to share our work on segmenting up to 35 organelles & macromolecular structures in whole cell isotropic FIB-SEM at 4 & 8nm resolution biorxiv.org/content/10.1101/β¦ 1/12
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COSEM retweeted
6 Oct 2021
Weβve also gotten a facelift! πββοΈ Browse all the related data for these papers and more - AND - volume renderings are now available for most segmentations. Check it out on openorganelle.janelia.org !
6 Oct 2021
Itβs official! Our manuscript is out today in @Nature. π₯³ 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!
rdcu.be/cy1UJ (1/3)
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COSEM retweeted
17 Jun 2021
Sounds like a great course!
17 Jun 2021
Final session of @bengurionu data science in cell imaging course!
Course summary and @OpenCellCZB, @OpenOrganelle, and @AllenInstitute public resources
Slides are up assafzar.wixsite.com/dsci202β¦, ping me for recordings!
Still curious to see how students' projects will turn out :-)
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28 May 2021
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28 May 2021
You might also consider using the free version of syGlass. syglass.io/view
It's significantly better with a VR headset, but the rendering is so choice. [Data credit to @COSEMdata ]
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COSEM retweeted
13 Apr 2021
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) authors.elsevier.com/c/1cv4Pβ¦
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COSEM retweeted
12 Feb 2021
Looks like I'll be spending a lot of time playing around with openorganelle.janelia.org/ soon!
Great talk from @avweigel with such beautiful pictures (as always) at #AIM2021
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COSEM retweeted
11 Feb 2021
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 π¬π©π»βπ» Happy #WomenScienceDay! #womenatjanelia #womeninscience 3/4
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COSEM retweeted
11 Feb 2021
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 π§«π¬π©π»βπ» Happy #WomenScienceDay! #womenatjanelia #womeninscience 2/4
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COSEM retweeted
11 Feb 2021
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 π§ͺππ§πΌβπ¬ Happy #WomenScienceDay! #womenatjanelia #womeninscience 1/4
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COSEM retweeted
9 Feb 2021
Amazing presentation at #AIMicroscopy Symposium: "Automatic whole cell organelle segmentation in volumetric electron microscopy" @avweigel
@HHMIJanelia @BogovicJohn @herrsaalfeld @herrsaalfeld et al.
openorganelle.janelia.org
#Unet #deeplearning #microscopy
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29 Jan 2021
This is dope!
29 Jan 2021
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 π¬
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23 Dec 2020
Thanks for the lovely write up @mariana_deniz in @preLights summarizing our recent preprint! prelights.biologists.com/higβ¦
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