Bugra Özdemir‡, Aastha Mathur§, Johanna Bischof§, John E. Eriksson|, Jean-Karim Hériché¶, Josh Moore#, Christian Tischer¤, Antje Keppler§Corresponding author: Bugra Özdemir ( bugra.oezdemir@embl.de ) Corresponding author: Antje Keppler ( antje.keppler@eurobioimaging.eu ) © Bugra Özdemir, Aastha Mathur, Johanna Bischof, John E. Eriksson, Jean-Karim Hériché, Josh Moore, Christian Tischer, Antje Keppler. This is an open access preprint distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Citation:
Özdemir B, Mathur A, Bischof J, Eriksson JE, Hériché J-K, Moore J, Tischer C, Keppler A (2023) BatchConvert: A command-line tool for parallelised conversion of image collections into the standard bioimage file formats OME-TIFF and OME-Zarr. ARPHA Preprints. https://doi.org/10.3897/arphapreprints.e116669 |  |
File formats incompatibility has become a major obstacle in biological imaging, complicating downstream processes such as image processing and analysis. One way to address this challenge is to convert the acquired image data into standard image file formats. Here we introduce BatchConvert, a command line tool for parallelised conversion of image collections into OME-TIFF or OME-Zarr using the workflow management system Nextflow. BatchConvert offers functionalities such as remote input-output support, optional execution on Slurm clusters and pattern-based filtering of input files. Conversion can be coupled to image concatenation, allowing selected images to be merged along specified dimensions. Support for remote locations includes an option to submit the output data to S3-compatible object stores or public archives such as BioImage Archive. Overall, BatchConvert is a flexible tool for researchers who are routinely managing and analysing large multidimensional image data that is either locally or remotely stored.