README

This Toolbox is built 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.

This project is forked from https://github.com/hermankhfung/3DCT

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.

This software is adapted for use at Rosalind franklin Institute, for our specific needs.

The Toolbox is written in Python 3.8 and uses PyQt5 GUI.

For development, conda/anaconda package manager is recommended. An environment file rfi-3dct-condaenvironment.yml is provided. A summary of library dependencies are:

pyqt [1]
numpy [1]
scipy [1]
matplotlib [1]
colorama [1]
tifffile [1]
opencv [1]
scikit-image [1]
psutil [1]
qimage2ndarray [2] (-c conda-forge)[1]
tools3dct [3]

[1]: Available via pip or conda or another your favourite package manager [2] Only available in conda-forge channel . Use >conda install qimage2ndarray -c conda-forge . [3]: Available via https://github.com/rosalindfranklininstitute/tools3dct/blob/main/setup.py. Clone it and run >python setup.py install

A test dataset can be downloaded here: https://3dct.semper.space/download/3D_correlation_test_dataset.zip

An introduction video can be viewed here: https://www.youtube.com/watch?v=nZnUZ877-TU

License

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/>.

Versions

Version 2.0 was the first public release, by Jan Arnold, the orignal author, in Python 2.7.
Version 2.4 contains bugfixes and documentation updates by Vladan Lucic, 2020.
Version 3.0 contains modifications by Herman Fung, 2021, including the porting of Version 2.4 to Python 3.8 and the addition of functions from tools3dct for fiducial position determination and post-correlation 3D transformations.

The most recent stable release version is 3.0.0.

Binaries

Binaries for macOS, Windows 7 and Windows 10, built using PyInstaller, are available at https://github.com/hermankhfung/3DCT/releases.

Past releases are available at https://3dct.semper.space/

Citing

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

jmp1985 / 3DCT