Difference between revisions of "Correct 3D Drift"

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This Fiji menu command is implemented by the script [http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=plugins/Scripts/Plugins/Registration/Correct_3D_drift.py;hb=HEAD "Correct 3D Drift"].
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{{ComponentStats:sc.fiji:Correct_3D_Drift}}This Fiji menu command is implemented by the script {{GitHub|org=fiji|repo=Correct_3D_Drift|path=src/main/resources/scripts/Plugins/Registration/Correct_3D_drift.py|label=Correct_3D_Drift.py}}.
  
1. The script expects the currently open and active image to be a hyperstack consisting of 2D or 3D volumes over time. The script registers the time points to each other using the phase correlation implementation of [[Imglib|ImgLib 1]].
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# The script expects the currently open and active image to be a hyperstack (or virtual hyperstack) consisting of 2D or 3D volumes over time. The script registers the time points to each other using the phase correlation implementation of [[Imglib|ImgLib 1]].
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# Once implemented a dialogue box will request the use to select the color channel to use for registration.
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# If memory is limiting on the system then the user can select to use a virtualstack for the result. 
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# If a virtualstack is selected the a folder save the aligned stack to needs to be selected.
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# After some processing (there are progress bars), the resulting, registered volumes are opened. If a virtualstack was selected the registered volume will already be saved in the chosen target folder.
  
2. Then, a folder is asked for, where the registered time point volumes will be stored.
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The script was originally written by {{Person|Albertcardona}} and [http://monash.edu/science/about/schools/biological-sciences/staff/bryson-richardson/ Robert Bryson-Richardson] while attending the [http://cwp.embo.org/pc10-37/ Developmental Imaging EMBO course] organized by [http://www.igc.gulbenkian.pt/research/photo/556/ Gabriel] [http://www.igc.gulbenkian.pt/research/unit/51 G. Martins].
  
3. The color channel to use for registration is asked for.
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== Publication ==
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* [http://http://www.jove.com/video/51086/sample-drift-correction-following-4d-confocal-time-lapse-imaging Parslow A, Cardona A and Bryson-Richardson RJ (2014) Sample drift correction following 4D confocal time-lapse imaging. J Vis Exp. 2014 Apr 12;(86). doi: 10.3791/51086].
  
4. After some processing (there are progress bars), the resulting, registered volumes are opened in a virtual hyperstack. They are already saved in the chosen target folder.
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[[Category:Plugins]]
 
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[[Category:Registration]]
The script was written by [[User:Albertcardona|Albert Cardona]] and [http://www.biolsci.monash.edu.au/staff/bryson-richardson/index.html Robert Bryson-Richardson] while attending the [http://cwp.embo.org/pc10-37/ Developmental Imaging EMBO course] organized by [http://www.igc.gulbenkian.pt/research/photo/556/ Gabriel] [http://www.igc.gulbenkian.pt/research/unit/51 G. Martins].
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[[Category:Citable]]

Latest revision as of 22:06, 2 June 2017

Correct 3D Drift
Project Fiji
URL https://imagej.net/Correct_3D_Drift
Source on GitHub
License GPLv3
Release 1.0.1
Date Sat Apr 29 22:37:37 CDT 2017
Development status Active
Support status Active
Team
Founders Albert Cardona
Leads Christian Tischer
Developers Christian Tischer
Debuggers Christian Tischer
Reviewers Christian Tischer
Support Christian Tischer
Maintainers Christian Tischer, Curtis Rueden
Contributors Albert Cardona, Robert Bryson-Richardson, Jan Eglinger

This Fiji menu command is implemented by the script Correct_3D_Drift.py.

  1. The script expects the currently open and active image to be a hyperstack (or virtual hyperstack) consisting of 2D or 3D volumes over time. The script registers the time points to each other using the phase correlation implementation of ImgLib 1.
  2. Once implemented a dialogue box will request the use to select the color channel to use for registration.
  3. If memory is limiting on the system then the user can select to use a virtualstack for the result.
  4. If a virtualstack is selected the a folder save the aligned stack to needs to be selected.
  5. After some processing (there are progress bars), the resulting, registered volumes are opened. If a virtualstack was selected the registered volume will already be saved in the chosen target folder.

The script was originally written by Albert Cardona and Robert Bryson-Richardson while attending the Developmental Imaging EMBO course organized by Gabriel G. Martins.

Publication