Fiji plugin to read Xradia files

XRM Reader    https://doi.org/10.5281/zenodo.7124263

 This is a plugin for Fiji (ImageJ) that reads *.xrm, *.txrm, and *.txm image files (from Xradia microCT systems, in their proprietary format, a form of OLE container) and opens them as image stacks, along with a text window displaying some metadata parameters. Download and extract the .zip folder and just drop the two jar files (poi-3.7.jar and XRM_Reader.jar) onto the Fiji main window. The program should put them in the right places. Restart Fiji and you should find it under Plugins > XRM Reader. If not, manually place poi-3.7.jar in Fiji.app/jars, and the XRM_Reader.jar in Fiji.app/plugins.

This code is publicly available at this link and free for anyone to use. If you use it in a publication, please cite the Zenodo doi above.  Current versions can also be found here:

https://ucloud.univie.ac.at/index.php/s/RSJ05Nb9FTViCVK

 

 

(I modified the above plugin from this one:  https://github.com/mrsutherland/XRM_Reader/releases by mrsutherland, 14 Nov 2017)

 

I have also included an ImageJ macro (XRM_files_thumbnails.ijm) that makes a preview image (PNG) and metadata file (.txt) with the same filename base as each unpreviewable *.xrm, *.txrm, or *.txm image file (examples below). The script automatically processes every Xradia-format image in a directory and its subdirectories.

 

This is in the ImageJ macro language and requires the XRM Thumbnails plugin, also included in the same archive. This plugin isn't meant to be run on its own, so I like to put XRM_Thumbnails.jar in the folder Fiji.app/plugins/Utilities, so that it does not appear in the Plugins menu, where it is confusing to see next to the XRM Reader plugin.

 

I like to put the .ijm macro in either Fiji.app/plugins/Scripts/File or Fiji.app/scripts/File, and then it appears in the File pull-down menu.

 

This version makes an XYZ montage for each reconstructed stack and a 0°+ 90° mugshot for each projection series (really first and middle projection: for a 360° scan it will be front and back images; my machine doesn't do full rotations). It now includes the date/time from .txrm files. (Fun fact: the container files *.xrm, *.txrm, or *.txm can be extracted to a bunch of hex files using 7‑Zip. I opened some of these with Hex Fiend or HxD to get the format of the date entry.)

 

Please note: the version of this macro I uploaded to Zenodo contains an error. Line 62 (in function ProcessFile) should be

         run("XRM Thumbnails", "load=[" + CurrentFile + "]");

not "XRM_Thumbnails" (underscore should be omitted). I will get around to re-uploading this some time.

 If you have questions or comments, feel free to contact me.

 Brian Metscher

Vienna, Dec. 2024

brian.metscher[at]univie.ac.at

 

 >> Note that Xradia .txm files can also be opened directly in Amira 6.4 and higher (Windows), and also in Drishti (https://github.com/nci/drishti). (Also in ORS Dragonfly Pro, but not in the free Dragonfly version.)

 

TXM-Wizard by fmeirer, liuyijin can open Xradia files also:  

      https://sourceforge.net/projects/txm-wizard/files/?source=navbar

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284347/

 

>> Real progress toward a Python solution can be found here: https://pypi.org/project/xrmreader/

It's based on the dxchange Python code, which seems to cover the reading of the xrm container files better than the Java parser:  https://github.com/data-exchange/dxchange

 

Sample outputs from the preview macro XRM_files_thumbnails.ijm: