Sustainability of Digital Formats: Planning for Library of Congress Collections
Sustainability of Digital Formats: Planning for Library of Congress Collections |
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| Introduction | Sustainability Factors | Content Categories | Format Descriptions | Contact | |
| Full name | Transmission X-Ray Microscopy (TXM), ZEISS proprietary microscopy data format |
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| Description |
TXM/TXRM are proprietary microscopy data files created by ZEISS 3D X-Ray Microscopes. As described in ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, "Datasets that contain a collection of projection images are saved as *.txrm files. Each *txrm file contains multiple images...When used, Reconstructor manually reconstructs images stored in each *txrm file to form a set of reconstructed slices. A slice is a 2D section of the 3D reconstructed volume that is oriented in the X/Z plane. Slices generated from each *.txrm file are stored in a *.txm file."
The ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, Table B-1, ZEISS File describes the package of files used in the program. Name extensions include:
Xradia Versa's Scout-and-Scan System is used to manage the process of data acquisition, from setting up, loading, scouting the region of interest (ROI), scanning, and acquiring the tomography. XMReconstructor, that accompanies ZEISS Xradia X-Ray CT scanners, is used to reconstruct TXRM projections, producing TXM image stack files. Per ZEISS' Press Release, ZEISS is Shaping the Future of Microscopy by Acquiring Xradia, July 2013, "The unique optical design allows the ZEISS Xradia Ultra and Versa series to cover a large resolution range, enabling the user to easily find the region of interest by zooming into larger samples (Scout-and-Zoom)." Transmission X-Ray Microscopy (TXM): As defined by Royal Society of Chemistry, Transmission X-Ray Microscopy is "an imaging technique where a finely focused beam of X-rays is directed at the specimen and the energies and intensities of the transmitted X-rays are measured as a function of position." According to Stephanie Spence in Transmission X-ray Microscopy and Its Applications in Battery Material Research--A Short Review, 2021, "...X-rays have the advantage of high penetration power and are capable of looking at internal structures in bulk materials...TXM measured the transmitted X-rays after passage through the sample. X-rays interact with electrons in the matter when passing through a sample...The intensity, energy and directions of the transmitted X-rays carry the sample information." ZIESS Xradia Versa's User Guide, File and File Storage, 2014-2016, states "X-ray microscopes form images based on the X-rays transmitted by the sample. Where the sample absorbs more X- rays, the image is darker; where it transmits more X-rays, the image is brighter. Absorption increases with density and thickness, and is also generally higher for elements with a higher atomic number in the periodic table. Magnification in X-ray microscopes is typically achieved either by using a projection geometry with a point source (as in the Xradia Versa), or by using optical elements similar to a regular visible light microscope (as in the Xradia Ultra)...In X-ray Computed Tomography (CT), the sample is images from different directions...A single image at one particular angle is referred to as a projection. Computer algorithms can be used to reconstruct the internal, 3-dimensional (3D) structure of the sample from a series of projections. The reconstructed volume can be visualized in different ways." Per ZEISS' Press Release, ZEISS is Shaping the Future of Microscopy by Acquiring Xradia, July 2013, "This acquisition further strengthens the position of the ZEISS Microscopy business group, the only manufacturer of light, electron and X-ray microscopes, with unique solutions for research and routine inspection in materials and life sciences application fields...X-ray microscopes show unique capabilities in materials research, allowing for 3D imaging of the internal structure of materials. Spatial resolution down to 50 nanometers can be achieved on a laboratory-based system. The non-destructive nature of X-ray imaging enables the observation and quantification of microstructural evolution in the same region of a single sample over time, or under changing environmental conditions." TXM/TXRM Files: According to the TXM Document, TXM Wizard Help, from TXM Team at Stanford Synchrotron Radiation Lightsource (no date found), "TXRM is a standard Xradia file format which is usually an image stack taken with a certain motor scan (e.g. focus series, and/or tomography data). A reference image may be included in the file. A header containing the information about the motor positions and etc. is also included in the '.txrm' file." GitLab.com user Martin Anderson personal project, txrmtools, 2019, "The purpose of this Python module is to extract information from .txrm data files from ZEISS Xradia Versa 3D X- ray microscopy scanners. The file format is essentially a Microsoft OLE2 container with a proprietary hierarchical structure that is specific to a family of ZEISS scanners...Disclaimer - This module is based on reverse engineering rather than a formal specification—users should exercise caution when using this module.". Note: the compilers of this resouce have not found other documentation to support this. Comments welcome. In the ResearchGate.net post, Re: Attributions to Enter in Dragonfly software for Raw Images Obtained from Micro CT Scan?, May 2022, user Mike Marsh states, “TXRM files are input for 3D reconstruction algorithm. The output of that reconstruction is a TXM image or DICOM stack or TIFF stack of CZI image which can be postprocessed in Dragonfly Pro.” Uses of TXM/TXRM Files: As described on ZEISS.com's X-Ray Microscopy Products page, "3D X-Ray Microscopes (XRM) provide superior 3D image quality and data for a wide range of materials and working environments." Application examples include:
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| Production phase | Middle to final state. TXM/TXRM files are used by the ZEISS Xradia 3D X-Ray Microscopes, TXRM files containing a collection of dataset images are used by the Reconstructor software to form 2D slices that are stored as TXM files. TXM files can be loaded into format supportive software to visualize and analyze the data. |
| LC experience or existing holdings | The Library of Congress has a small number of TXM files in its collections. |
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| LC preference | See the Library of Congress Recommended Formats Statement for format preferences for 3D content. |
| Disclosure | Proprietary dataset format. As stated in the ZIESS Xradia Versa's User Guide, File and File Storage, 2014-2016, TXM is a "3D tomography volume dataset file in proprietary ZEISS format." Comments welcome. |
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| Documentation |
No formal specification but informal information on format obtained in the ZIESS Xradia Versa's User Guide, File and File Storage, 2014-2016. Other useful TXM/TXRM format information found:
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| Adoption |
According to Xianghui Xiao in TXM-Sandbox: An Open-Source Software for Transmission X-Ray Microscopy Data Analysis, 2021, “TXM data processing depends on the type of data. Different types of TXM require different analysis processes and prerequisites for each individual process step...There are a few software programs either dedicated to or capable of TXM data analysis.”
Other TXM/TXRM post-processing software:
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| Licensing and patents |
Per ZIESS Xradia Versa's User Guide, File and File Storage, 2014-2016, “Carl Zeiss X- Ray Microscopy retains the patent rights to any and all processes and inventions developed during the course of performing work for the customer, unless specifically identified to the contrary in advance by the customer. The fact that this guide includes a copyright notice does not in any way affect the proprietary status of this guide... Raad and Scout-and-Scan are trademarks and Xradia Ultra, Xradia Versa, ZEISS, Carl Zeiss, and the ZEISS logo are registered trademarks of CARL ZEISS AG CORPORATION.” |
| Transparency |
nanoFAB Knowledge Base's ZEISS Xradia Versa 620 Workflow - Staff Analysis, last modified May 2022, provides staff with instructions for sample submitting and data processing when using the Xradia Versa 620. The workflow describes the "other file formats available: 2D projection files (.xrm), reconstructed raw files (.txm), projection dataset (.txrm) and recipe file (.rcp). Most of these files are Zeiss proprietary and need special versions of software to open." See Adoption for more information on software that can open, read, and analyze TXM/TXRM data files. |
| Self-documentation |
TXM/TXRM files contain some form of metadata, but limited information found about the metadata contained. Zenodo.org, a general-purpose open repository for related digital artefacts, HDTomo TXRM Micro-CT Datasets, May 2021, has a collection of 6 individual micro Computed Tomography datasets, stating files contains "all raw projection and reconstructed volume data both in the native ZEISS TXRM/TXM format...The TXRM contains the raw projection data as well as metadata specifying the scan geometry. The TXM contains the vendor volume reconstruction.” |
| External dependencies |
Per ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, "The Xradia Versa includes the hardware and software needed to create and view tomography images." Comments welcome. |
| Technical protection considerations |
Per ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, Proprietary Notice, "The material contained herein consists of information that is the property of Carl Zeiss X-ray Microscopy, and intended solely for customer use in operating the system (Xradia Versa) described in this guide. This guide or any part of it must not be translated, reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information or retrieval system. Violators will be prosecuted...The use of general descriptive names, registered names, trademarks, etc. in this guide does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Software programs will fully remain the property of Carl Zeiss X-ray Microscopy. No program, documentation, or subsequent upgrade thereof may be disclosed to any third party, unless prior written consent of Carl Zeiss X-ray Microscopy has been procured to do so, nor may they be copied or otherwise duplicated, even for the customer’s internal needs apart from a single backup copy for safety purposes. |
| Other | |
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| 3D Model Geometry |
According to the ZEISS Catalog, Maintain High Resolution at Large Working Distances, 2021 (Downloadable PDF Link), the “Dragonfly Pro program supports regular and unstructured surface meshes and contains advanced editing tools to create regions of interest from a mesh and vice versa.” Limited information on specifics relating to other programs. |
| 3D Model Appearance |
According to the ZEISS Catalog, Maintain High Resolution at Large Working Distances, 2021 (Downloadable PDF Link), the Dragonfly Pro software tools can be trailered for optimal workflow, allowing users to “control registration, map differences, and customize the appearance” of TXM files. Limited information on specifics relating to other programs. |
| 3D Model Scene |
Little to no information is found on 3D model scene, light source, camera, or position. Different post-processing software may have different options or settings. |
| 3D Model Animation |
Little to no information is found on 3D model animation. Different post-processing software may have different options or settings for animation. |
| Tag | Value | Note |
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| Filename extension | txm |
ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, Table B-1. See https://www.physics.purdue.edu/xrm/new-users/training/Xradia_Versa_Users_Guide_v11x_510.pdf. |
| Filename extension | txrm |
ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, Table B-1. See https://www.physics.purdue.edu/xrm/new-users/training/Xradia_Versa_Users_Guide_v11x_510.pdf. |
| Filename extension | xrm |
ZEISS Xradia Versa's User Guide, File and File Storage, 2014-2016, Table B-1. See https://www.physics.purdue.edu/xrm/new-users/training/Xradia_Versa_Users_Guide_v11x_510.pdf. |
| Pronom PUID | See note. | No Pronom PUID as of May 2023. |
| Wikidata Title ID | See note. | No Wikidata entry as of May 2023 |
| General | |
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| History |
Per Carl ZEISS AG Wikipedia page, ZEISS, the manufacturer of optical systems and optoelectronics, was founded in Germany in 1846 by optician Carl Zeiss, joined later by Ernst Abbe, and Otto Schott. The company is multi-national and is active business segments Industrial Quality and Research, Medical Technology, Consumer Markets, and Semiconductor Manufacturing Technology. |
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