TXM_Sandbox

This is a GUI program based on Jupyter that integrates tomography reconstruction and 2D/3D XANES data analysis. It provides a mechanism that allows users to customize the input data file formats.

Installation (Linux)

via conda-forge

conda create -n pytxm python=3.10 txm_sandbox -c conda-forge
conda activate pytxm

Installation (Windows)

Revised for Windows by Adrian Francisco Duran Ornelas, [email protected], @afornelas

Install miniconda3 from https://docs.conda.io/projects/miniconda/en/latest/index.html

Open the Anaconda Powershell Prompt (miniconda3) and run

conda create -n pytxm python=3.8 txm_sandbox -c conda-forge
conda activate pytxm

Usage

You also need to install Fiji/ImageJ in your computer. After installing Fiji, you will need to update ImageJ then Fiji from its 'Help' menu. Restart Fiji after the updates.

You will need to copy TXM_GUI2.ipynb into a working directory. Change to that working directory, then run

jupyter lab

This will launch Jupyter in your preferred web browser. The first cell in the opened Jupyter notebook is for launching TXM_Sandbox GUI. The second line

gui = txmg.txm_gui(fiji_path='/home/xiao/software/Fiji.app', form_sz=[750, 1000])

includes the Fiji path as its argument. Change the path to your Fiji installation path. Click on the first cell and do shift+enter will run this cell. This will bring up TXM_Sandbox GUI.

References:

Please cite these two papers if you use TXM_Sandbox in your works.

1. Xiao, X., Xu, Z., Lin, F. & Lee, W.-K., "TXM-Sandbox: an open-source software for transmission X-ray microscopy data analysis" (2022). J. Synchrotron Rad. 29, 266-275. https://doi.org/10.1107/S1600577521011978

2. Xiao, X., Xu, Z., Hou, D., Yang, Z. & Lin, F., "Rigid registration algorithm based on the minimization of the total variation of the difference map" (2022). J. Synchrotron Rad. 29, 1085-1094. https://doi.org/10.1107/S1600577522005598