tomopy-ij

tomopy-ij provides ImageJ support to tomopy.

tomopy-ij is derived from the TOMCAT recomanager developed by Federica Marone at the Swiss Light Source as described here and it is customized to provide similar functionality to the APS beamlines using tomoScan.

Installation

First, you must have Conda and Fiji with the PSI hdf plugin installed. Next install tomopy:

$ conda create --name tomopy --channel conda-forge tomopy

and activate this environment with:

$ conda activate tomopy

then install dxchange:

$ conda install -c conda-forge dxchange

and install tomopy cli

$ git clone https://github.com/tomography/tomopy-cli.git
$ cd tomopy-cli
$ python setup.py install

Finally

$ cd your_working_directory
$ git clone https://github.com/xray-imaging/tomopy_ij.git

Modify tomopy_ij.py sys.path.append() to point to:

sys.path.append('your_working_directory/tomopy-ij/tomopy_ij')

Usage

Locate the installation directory of the Fiji application (FIJI_DIR) and start Fiji from the same terminal where the tomopy conda env has been activated:

$ (`FIJI_DIR`)/Contents/MacOS(*)/ImageJ-macosx

(*) folder name will match the Operative System of your installation.

then File/Open and select the tomopy_ij/tomopy_ij.py and hit run:

to obtain the main tomopy_ij control screen:

Once you select a valid tomographic data set the projection data will be displayed in ImageJ as a stack:

Select Expert or Paganin to access additional parameters:

Press preview, try of full to reconstruct your data set: