@COSEMdata

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

 Virginia, USA
janelia.org/project-team/cosem
Joined November 2020
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  • Following97
  • Followers145
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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
organelle segmentation

ALT organelle segmentation

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Last Friday @CmHulbert presented #Paintera at #I2K2022 . Here, showing some beautiful @COSEMdata on openorganelle.org/ youtube.com/watch?v=rNJotgwU… github.com/saalfeldlab/paint…
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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!
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Come work with us at @HHMIJanelia with the new 🖌 Annotation & Analytics 📊 team tinyurl.com/5xxy2v95. This is a ✨ NEW ✨ multi-disciplinary team that will work with a variety of datasets (1/6)
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Still hiring for these positions at Janelia!
Marius Pachitariu@marius10p7 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-l…
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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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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! rdcu.be/cy1UJ (1/3)
Aubrey Weigel@avweigel17 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/… 1/12
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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 openorganelle.janelia.org !
Aubrey Weigel@avweigel6 Oct 2021
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! rdcu.be/cy1UJ (1/3)
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Sounds like a great course!
Assaf Zaritsky@AssafZaritsky17 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/dsci202…, ping me for recordings! Still curious to see how students' projects will turn out :-)

Data Science in Cell Imaging course | Assaf Zaritsky | Ben-Gurion University

Bridging computer science and cell biology. This course will review the state-of-the-art in visualizing, processing, integrating and mining massive cell image data sets, deciphering complex patterns...

assafzar.wixsite.com
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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/1cv4P…
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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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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
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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
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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
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Check out @COSEMdata and openorganelle.janelia.org/
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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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I don't know if you have played a bit with the database that @COSEMdata has created but... it is close to becoming orgasmic openorganelle.janelia.org/or… Here the two centrioles in Jurkat cells. Could you draw the pericentriolar region? Why? I am really enjoying this game!
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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/… 1/12 – at Lansdowne, VA
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