Spine align imags to root serial#

If you have a large image data set (~300 images or more), you will fill up your disk quota before saving cropped images. Make sure to clear unused files before starting a new alignment because you can end up with ~700 GB of data at the end of a single alignment project. There is a disk quota for your work folder on stampede2 (1 TB?).This will open your work folder, named with a 5-digit number, e.g.: /work2/#/yourname/stampede2. In the next prompt, enter 6-digit number on your TACC Token app. At the prompt, enter your TACC password.Click 'Save' if you have not done so already.

Set up a New Site: File protocol = SCP Host name = Port number = 22, User name = your TACC username.

ДЄrt Wetzel's presentation at NeuroNex Workshop (July, 2018)ДЎ.В Upload your files from your local drive (Windows PC) Lichtman (2016) Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening. Wetzel, Jennifer Bakal, Markus Dittrich, David G. (2016) The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus. (2017) Whole-brain serial-section electron microscopy in larval zebrafish.

Spine align imags to root serial#

SWiFT-IR has been used to align serial EM images for: ДЄlignEM-SWiFT is an implementation of SWiFT-IR (Signal Whitening Fourier Transform Image Registration), developed by Art Wetzel, Tom Bartol, and Bob Kuczewski. We also have a protocol for using TrakEM2. Reconstruct has a method for manual alignment (outlined in Ch 10 of the Reconstruct User Manual), but it is time-consuming and does not produce the best results. While Reconstruct can determine synapse area and trace volume regardless of alignment, good alignment is important for many reasons: Alignment is essential for serial section EM.