http://capture-clarity.org/capture daily 1.0 2016-06-17 https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934ef669492ec8d74a8e37/1464421403726/ Introduction Schematic of ArcTRAP labeling and the enhanced cohort-scale CLARITY pipeline for rapid whole brain clearing and imaging https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934f1c4bf1182ee606f2af/1464421439810/ Introduction Schematic of viral labeling (top). Three-dimensional rendering of a CLARITY mouse hemisphere, visualizing outgoing mPFC projections (lower left) and example of CLARITY-based tractography (lower right). https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/5763a043893fc07fb7f01f51/1466146904537/ Introduction On tCELL https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/5693726f05f8e207078d96d2/1452503665173/b3.png Introduction http://capture-clarity.org/optimized-clarity daily 0.75 2016-06-23 https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934b3ed82d5eff6cc83c4b/1452493637851/ftc2.png Optimized CLARITY Alternative flow-assisted clearing setup without using a circulator. A 50ml conical tube (with small holes drilled in the middle and on the bottom, as indicated by red arrows) can be inserted into a 250ml glass bottle filled with clearing buffer. Each tube fits 3-4 mouse brains. Unidirectional flow (blue line) is created by using a magnetic stir bar and a stirring hot plate to accelerate the clearing. Upon first use, the temperature of the hot plate needs to be set properly so that the buffer temperature is maintained at desired level inside the conical tube. https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934ae15a566828b96ef634/1452493551931/ Optimized CLARITY Setup of parallel flow-assisted clearing. Up to 4 mouse brains can be inserted into a tissue cassette (30x40x12mm). Two cassettes (indicated by red arrows) are inserted into a chamber constructed with an inlet and outlet for buffer exchange. To scale up clearing, multiple chambers (each containing up to 8 brains) can be connected in parallel to a temperature-controlled circulator (calibrated so that the temperature in the sample chamber is kept at 40°C). http://capture-clarity.org/imaging daily 0.75 2016-01-11 https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934c19bfe873d739490ebc/1452493851048/ Imaging Schematic and picture of the adapter used for mounting brains onto the ultramicroscope https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934c3acbced6b74bd029f7/1452493903765/ Imaging Left: three-dimensional rendering of a CLARITY-processed whole mouse brain (ArcTRAP), White: tdTomato signal. Scale bar, 500 µm. Right: Top: single FOV images at indicated imaging depths. Bottom: zoomed in images from the yellow-boxed regions in the top row, showing cellular resolution. Scale bar, 100 µm. http://capture-clarity.org/analysis-pipeline daily 0.75 2016-01-13 https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934cc4cbced6b74bd02c25/1452494025618/ TRAP Analysis Pipeline Data processing pipeline for image registration, cell detection, annotation and quantification http://capture-clarity.org/contact-and-links daily 0.75 2016-01-11 http://capture-clarity.org/clarity-based-tractography daily 0.75 2016-05-28 https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/56934d8e7086d7242734965a/1452494237189/ CLARITY-based Tractography a, Raw CLARITY image, showing outgoing mPFC projections (EYFP). b, Image intensity gradient amplitude, computed by convolving the 3-dimensional CLARITY image volume with three 3-dimensional 1st order derivative of Gaussian functions, c, Color-coded principal fiber orientations (A-P: red; D-V, green; L-M, blue), estimated as the tertiary eigenvectors of computed structure tensors. For better visualization, the color brightness was weighted by the raw CLARITY image intensity. Scale bars in a-c: 100 µm. d, A zoomed-in region of (c) showing the principal fiber orientations as color-coded vector fields overlaid on raw CLARITY image. The vectors are color-coded for their orientation. Scale bar: 6µm. https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/5693459ca12f449cd65aa00d/1452492204901/ CLARITY-based Tractography https://static1.squarespace.com/static/569327c3e0327c8c4234364b/t/5693455fa976af0bfc5b597f/1452492127448/ CLARITY-based Tractography http://capture-clarity.org/image-gallery-1 daily 0.75 2016-05-28 https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/56935a141115e0dc633f1bff/1464421847193/whole_right.png Image Gallery - 3D mPFC projection (CLARITY hemisphere) imaged by 2X objective at 0.8x zoom with a single FOV, Grid size: 500um https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/56935a7f69a91a378990f676/1464421862392/3ROIs.png Image Gallery - Isolating mPFC projection Computational isolation of mPFC fibers that project to VTA (yellow) or BLA (green). https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/56935a7f0ab377deeedb93d4/1464421859897/trac_whole.png Image Gallery - Whole brain CLARITY-based tractography The streamlines are color-coded for orientation. A-P: red; D-V, green; L-M, blue https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/56935a8d25981daa98fed5a4/1464421856286/v214.png Image Gallery - Visualizing mPFC to VM projection in 3D showing tracts turning near the VTA. Grid size: 500um https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/56935ab525981daa98fed64c/1464421840857/whole_adj.png Image Gallery - 3D rendering of a whole TRAP brain White: tdTomato signal. Grid size: 500um https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/56935fe27086d7242734e6b1/1464421849478/seed.png Image Gallery - Reconstruction of axonal fibers from CLARITY Left: raw image. Right: streamlines reconstructed by structural tensor-based tractography. Fibers in the CLARITY image that did not pass the user-defined seed region (orange) were excluded in the reconstruction (magenta arrows) https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/569365bfa128e6b30eb4ad4c/1464421853243/longlong.png Image Gallery - Visualizing mPFC to VM projection in 3D Tracking mPFC to VM projection over 6mm https://static1.squarespace.com/static/569327c3e0327c8c4234364b/56935a140ab377deeedb9225/57494cd807eaa01052195f3c/1464421844752/CLARITY_1_PFC.png Image Gallery - 3D mPFC projection (CLARITY hemisphere) http://capture-clarity.org/movies daily 0.75 2016-05-28 http://capture-clarity.org/oeg daily 0.75 2016-06-26