Filter
Associated Lab
- Ahrens Lab (2) Apply Ahrens Lab filter
- Aso Lab (1) Apply Aso Lab filter
- Betzig Lab (2) Apply Betzig Lab filter
- Beyene Lab (1) Apply Beyene Lab filter
- Branson Lab (2) Apply Branson Lab filter
- Card Lab (1) Apply Card Lab filter
- Cardona Lab (5) Apply Cardona Lab filter
- Clapham Lab (1) Apply Clapham Lab filter
- Dickson Lab (2) Apply Dickson Lab filter
- Dudman Lab (2) Apply Dudman Lab filter
- Espinosa Medina Lab (2) Apply Espinosa Medina Lab filter
- Feliciano Lab (1) Apply Feliciano Lab filter
- Funke Lab (3) Apply Funke Lab filter
- Harris Lab (2) Apply Harris Lab filter
- Heberlein Lab (1) Apply Heberlein Lab filter
- Hermundstad Lab (3) Apply Hermundstad Lab filter
- Hess Lab (5) Apply Hess Lab filter
- Jayaraman Lab (1) Apply Jayaraman Lab filter
- Karpova Lab (1) Apply Karpova Lab filter
- Keller Lab (2) Apply Keller Lab filter
- Lavis Lab (10) Apply Lavis Lab filter
- Lee (Albert) Lab (1) Apply Lee (Albert) Lab filter
- Lippincott-Schwartz Lab (14) Apply Lippincott-Schwartz Lab filter
- Liu (Zhe) Lab (6) Apply Liu (Zhe) Lab filter
- Looger Lab (11) Apply Looger Lab filter
- O'Shea Lab (1) Apply O'Shea Lab filter
- Pachitariu Lab (6) Apply Pachitariu Lab filter
- Podgorski Lab (1) Apply Podgorski Lab filter
- Reiser Lab (3) Apply Reiser Lab filter
- Romani Lab (4) Apply Romani Lab filter
- Rubin Lab (4) Apply Rubin Lab filter
- Saalfeld Lab (4) Apply Saalfeld Lab filter
- Scheffer Lab (2) Apply Scheffer Lab filter
- Schreiter Lab (1) Apply Schreiter Lab filter
- Spruston Lab (3) Apply Spruston Lab filter
- Stern Lab (5) Apply Stern Lab filter
- Sternson Lab (3) Apply Sternson Lab filter
- Stringer Lab (2) Apply Stringer Lab filter
- Svoboda Lab (7) Apply Svoboda Lab filter
- Tebo Lab (1) Apply Tebo Lab filter
- Tervo Lab (1) Apply Tervo Lab filter
- Tillberg Lab (3) Apply Tillberg Lab filter
- Truman Lab (3) Apply Truman Lab filter
- Turaga Lab (12) Apply Turaga Lab filter
- Turner Lab (1) Apply Turner Lab filter
- Zlatic Lab (1) Apply Zlatic Lab filter
Associated Project Team
Associated Support Team
- Cryo-Electron Microscopy (3) Apply Cryo-Electron Microscopy filter
- Electron Microscopy (1) Apply Electron Microscopy filter
- Fly Facility (3) Apply Fly Facility filter
- Integrative Imaging (2) Apply Integrative Imaging filter
- Janelia Experimental Technology (2) Apply Janelia Experimental Technology filter
- Molecular Genomics (2) Apply Molecular Genomics filter
- Primary & iPS Cell Culture (1) Apply Primary & iPS Cell Culture filter
- Project Technical Resources (3) Apply Project Technical Resources filter
- Quantitative Genomics (1) Apply Quantitative Genomics filter
- Scientific Computing Software (1) Apply Scientific Computing Software filter
- Viral Tools (2) Apply Viral Tools filter
Publication Date
- December 2021 (19) Apply December 2021 filter
- November 2021 (15) Apply November 2021 filter
- October 2021 (12) Apply October 2021 filter
- September 2021 (14) Apply September 2021 filter
- August 2021 (15) Apply August 2021 filter
- July 2021 (17) Apply July 2021 filter
- June 2021 (10) Apply June 2021 filter
- May 2021 (20) Apply May 2021 filter
- April 2021 (20) Apply April 2021 filter
- March 2021 (7) Apply March 2021 filter
- February 2021 (12) Apply February 2021 filter
- January 2021 (13) Apply January 2021 filter
- Remove 2021 filter 2021
174 Janelia Publications
Showing 171-174 of 174 resultsVoltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (>800MB/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present VolPy, an automated and scalable pipeline to pre-process voltage imaging datasets. VolPy features motion correction, memory mapping, automated segmentation, denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation, we introduce a corpus of 24 manually annotated datasets from different preparations, brain areas and voltage indicators. We benchmark VolPy against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that VolPy's performance in spike extraction and scalability are state-of-the-art.
Cells contain hundreds of organelles and macromolecular assemblies. Obtaining a complete understanding of their intricate organization requires the nanometre-level, three-dimensional reconstruction of whole cells, which is only feasible with robust and scalable automatic methods. Here, to support the development of such methods, we annotated up to 35 different cellular organelle classes-ranging from endoplasmic reticulum to microtubules to ribosomes-in diverse sample volumes from multiple cell types imaged at a near-isotropic resolution of 4 nm per voxel with focused ion beam scanning electron microscopy (FIB-SEM). We trained deep learning architectures to segment these structures in 4 nm and 8 nm per voxel FIB-SEM volumes, validated their performance and showed that automatic reconstructions can be used to directly quantify previously inaccessible metrics including spatial interactions between cellular components. We also show that such reconstructions can be used to automatically register light and electron microscopy images for correlative studies. We have created an open data and open-source web repository, 'OpenOrganelle', to share the data, computer code and trained models, which will enable scientists everywhere to query and further improve automatic reconstruction of these datasets.
Cells in many tissues, such as bone, muscle, and placenta, fuse into syncytia to acquire new functions and transcriptional programs. While it is known that fused cells are specialized, it is unclear whether cell-fusion itself contributes to programmatic-changes that generate the new cellular state. Here, we address this by employing a fusogen-mediated, cell-fusion system to create syncytia from undifferentiated cells. RNA-Seq analysis reveals VSV-G-induced cell fusion precedes transcriptional changes. To gain mechanistic insights, we measure the plasma membrane surface area after cell-fusion and observe it diminishes through increases in endocytosis. Consequently, glucose transporters internalize, and cytoplasmic glucose and ATP transiently decrease. This reduced energetic state activates AMPK, which inhibits YAP1, causing transcriptional-reprogramming and cell-cycle arrest. Impairing either endocytosis or AMPK activity prevents YAP1 inhibition and cell-cycle arrest after fusion. Together, these data demonstrate plasma membrane diminishment upon cell-fusion causes transient nutrient stress that may promote transcriptional-reprogramming independent from extrinsic cues.