Electron microscopic reconstruction of the mouse dorsal lateral geniculate nucleus

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Accessing the Data

Description of the dataset

Guide to structures in the dLGN dataset

Project Registry

View the quarter resolution data in a web browser HERE.
Viewer navigation:
    Move through sections = 'w', 's'
Move laterally = mouse drag
    Zoom = mouse scroll (zoom in and out), left click mouse (zoom in), 'shift' + left click mouse (zoom out)

Software links:
VAST - Manual segmentation software
WaferMapper - Matlab image acquisition package
lgnNautilus - All Matlab code used to analize the dLGN dataset for "The fuzzy logic of network connectivity in mouse visual thalamus."

This site is intended to provide public access to the data and analytical tools presented in "The fuzzy logic of network connectivity in mouse visual thalamus" Morgan JL, Berger DB, Wetzel AW, Lichtman JW. Cell (2016), doi: 10.1016/j.cell.2016.02.033. Two versions of the dataset are available for viewing: 1) The full resolution aligned dataset (alignment and upload in progress) and 2) The quarter resolution (S4) image aligned image volume. The quarter resolution image volume was used the nearly all of the current (as of 9/16/15) tracings. These tracings can also be viewed and edited using VAST. If you wish to add segmentation to the database contact Josh Morgan (joshmorgan@fas.harvard.edu). If you wish to perform additional research on this dataset and you want to avoid duplicating (as opposed to replicating) the work of others, we can list you on the project registry.

Accessing the data through VAST and our remote image server

Step 1: Download image viewing and segmentation software.

VAST version 1.01 (NOTE: Earlier versions of VAST will not support remote viewing.)

Step 2: Download '.vsvr' files which will allow VAST 1.01 to remotely view image volumes (via a Butterfly image server). Viewing segmentations (step 3) requires first linking to the matched EM volume (ie. dLGN-S4).

dLGN-Full: '.vsvr' file for the full resolution aligned LGN dataset (NOTE: Sections are being processed for uploading)

dLGN-S4: '.vsvr' file for the quarter resolution image data (S4). (NOTE: Some parts of this image volume may be unavailable as sections are still being uploaded)

Step 3: Download the desired segmentation file

dLGN-S4 Network This is the primary segmentation file for network tracing. NOTE: This file unzips to more than 70GB.

dLGN-S4 Instruction This segmentation file was created to teach users how to identify structures in the dLGN EM volume.

Step 4: Open data in VAST

Start VAST

Go to "File-> Open EM Stack..." and open the downloaded VAST '.vsvr' image volume pointer

Go to "File-> Open Segmentation ..." and open the downloaded and unzipped VAST '.vss' segmentation file.

Navigate, view and edit according to VAST instructions

NOTE: edge sections may be duplicates so try jumping to the center of the volume if it looks like sections are not changing.

Optional Matlab analysis code

NautilusAnalysis 1.4 Matlab code used for rendering and and analyzing VAST segmentations.

Credits
The creation and maintenance of the dLGNs1 database is the result of a collaboration between the labs of Jeff Lichtman and Hanspeter Pfister at Harvard University.

Image acquisition and analysis -Josh Morgan, Lichtman lab, Harvard.
Alignment of the S4 image volume - Art Wetzel, Pittsburgh Super Computing
Alignment of the full resolution image volume - Adi Peleg
VAST software development - Daniel Berger, Lichtman lab, Harvard
Image server creation and management - Daniel Haehn, Hanspeter Pfister Lab, Harvard
Segmentors - Josh Morgan, Daniel Berger, Linda Xu, Jacob Wasag, Aidan Piper, Seaun Yoo, Shana Attar, Katherine Mateos, Abigail Orlando, Anne Crosby, Kyla Cordrey, Allan Ordonez, Marquise Bartley