HitachiTEMTIFF_to_OME-TIFF
Description
This tool converts Hitachi TEM .tif images and matching .txt metadata files into OME-TIFF format. It requires Java (JRE 17 or above). This application includes the Bio-Formats library for writing OME-TIFF. The releases and source code are available from GitHub. The release downloads are in the 'Assets' sections at the bottom of the pages.
The Windows release is an .exe file that is moved into the same directory as the images to be converted.
The cross-platform release is a .jar file that is also run from the same directory as the images to be converted.
Metadata Mapping
Standard OME fields:
- PixelSize → Pixels.PhysicalSizeX/Y
- StagePositionX/Y/Z → Plane.PositionX/Y/Z
- Magnification → Objective.NominalMagnification
- Date and Time → Image.AcquisitionDate
All other metadata is stored as structured annotations.
Notes
- Pixel dimensions are converted from nanometers (Hitachi metadata) to micrometers (OME standard)
- Existing .ome.tif files are not overwritten
- Some TEM-specific fields are not defined in the OME standard and are stored as annotations
Compatibility
It has been tested on images created by Hitachi TEM system, Model HT7800, System Software Version 1.20, and AppCameraControl_HT7800 version 1.17.03.59.
Disclaimer
This software is not affiliated with, endorsed by, or supported by Hitachi High-Technologies or any of its affiliates.
The use of the name "Hitachi" refers solely to the format of the input data and does not imply any association with the company.
Assistance with this dataset
We welcome researchers wishing to reuse our data to contact the creators of datasets. If you are unfamiliar with analysing the type of data we are sharing, have questions about the acquisition methodology, need additional help understanding a file format, or are interested in collaborating with us, please get in touch via email. Our current members have email addresses on our main site. The corresponding author of an associated publication, or the first or last creator of the dataset are likely to be able to assist, but in case of uncertainty on who to contact, email Ben Micklem, Research Support Manager at the MRC BNDU.
Year Published
2026
DOI
10.60964/rnd-30fh-4k59
Metadata
Funders
Medical Research Council, UKRI (UKRI/MR/B000936/1)
Publisher
University of Oxford
Downloaded times
Group
Terms
Distributed under the GNU General Public License (GPL) version 2.0.