This Toolbox is build for 3D correlative microscopy. It helps with 3D to 2D correlation of three dimensional confocal image stacks to two dimensional SEM/FIB dual beam microscope images. Though it is not limited to that.
The 3D Correlation Toolbox was developed at the Max Planck Institute of Biochemistry, Department of Molecular Structural Biology on the basis of the paper Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy. 3DCT uses code from 3D rigid transformation from Pyto.
Further information can be found on http://www.biochem.mpg.de/en/rd/baumeister and http://3dct.semper.space
The Toolbox is written in Python 2.7 and comes with a PyQt4 GUI. Further dependencies as of now are:
- PyQt4 1
- numpy 2
- scipy 2
- matplotlib 2
- opencv 1
- cv2 2
- tifffile 0.9.2 2 (Christoph Gohlke)
- colorama 2 (optional for colored stdout when debugging)
- qimage2ndarray 2
A test dataset can be downloaded here: http://3dct.semper.space/download/3D_correlation_test_dataset.zip
An introduction video can be viewed here: https://www.youtube.com/watch?v=nZnUZ877-TU
Copyright (C) 2016 Jan Arnold
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
Version 2.0 is the first public release and received a revised GUI and image stack handling (reslicing) done in python (formerly outsourced to FIJI)
Most recent stable release version is 2.4.0.
There are Pyinstaller binaries available for Mac OS X, Windows, and Linux (built under Ubuntu 15.04) at http://3dct.semper.space/
We ask users to cite:
- The general paper that forms the basis of the 3D Correlation Toolbox
- When using independent modules/scripts from the source code, any specific publications of modules/scripts used in this software
- Check the header of the module/script in question for more detailed information
If journal reference limits interfere, the module/script-specific publications should take precedence.
In general, please cite this project and the modules/scripts used in it.
Thank you for your support!
Who do I talk to?
- Repo owner or admin
- Other community or team contact