PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved]
Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and publication accor...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wellcome
2020-08-01
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| Series: | Wellcome Open Research |
| Online Access: | https://wellcomeopenresearch.org/articles/5-96/v2 |
| _version_ | 1819006817213087744 |
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| author | Johnny Hay Eilidh Troup Ivan Clark Julian Pietsch Tomasz Zieliński Andrew Millar |
| author_facet | Johnny Hay Eilidh Troup Ivan Clark Julian Pietsch Tomasz Zieliński Andrew Millar |
| author_sort | Johnny Hay |
| collection | DOAJ |
| description | Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and publication according to open research principles. We present PyOmeroUpload, a Python toolkit for automatically extracting metadata from experiment logs and text files, processing images and uploading these payloads to OMERO servers to create fully annotated, multidimensional datasets. The toolkit comes packaged in portable, platform-independent Docker images that enable users to deploy and run the utilities easily, regardless of Operating System constraints. A selection of use cases is provided, illustrating the primary capabilities and flexibility offered with the toolkit, along with a discussion of limitations and potential future extensions. PyOmeroUpload is available from: https://github.com/SynthSys/pyOmeroUpload. |
| first_indexed | 2024-12-21T00:14:42Z |
| format | Article |
| id | doaj.art-9e4745c2544d4b9e81928075b47d6cf6 |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-12-21T00:14:42Z |
| publishDate | 2020-08-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj.art-9e4745c2544d4b9e81928075b47d6cf62022-12-21T19:22:16ZengWellcomeWellcome Open Research2398-502X2020-08-01510.12688/wellcomeopenres.15853.217849PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved]Johnny Hay0Eilidh Troup1Ivan Clark2Julian Pietsch3Tomasz Zieliński4Andrew Millar5EPCC, University of Edinburgh, Edinburgh, EH9 3FD, UKEPCC, University of Edinburgh, Edinburgh, EH9 3FD, UKSynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UKSynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UKSynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UKSynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UKTools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and publication according to open research principles. We present PyOmeroUpload, a Python toolkit for automatically extracting metadata from experiment logs and text files, processing images and uploading these payloads to OMERO servers to create fully annotated, multidimensional datasets. The toolkit comes packaged in portable, platform-independent Docker images that enable users to deploy and run the utilities easily, regardless of Operating System constraints. A selection of use cases is provided, illustrating the primary capabilities and flexibility offered with the toolkit, along with a discussion of limitations and potential future extensions. PyOmeroUpload is available from: https://github.com/SynthSys/pyOmeroUpload.https://wellcomeopenresearch.org/articles/5-96/v2 |
| spellingShingle | Johnny Hay Eilidh Troup Ivan Clark Julian Pietsch Tomasz Zieliński Andrew Millar PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved] Wellcome Open Research |
| title | PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved] |
| title_full | PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved] |
| title_fullStr | PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved] |
| title_full_unstemmed | PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved] |
| title_short | PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO [version 2; peer review: 2 approved] |
| title_sort | pyomeroupload a python toolkit for uploading images and metadata to omero version 2 peer review 2 approved |
| url | https://wellcomeopenresearch.org/articles/5-96/v2 |
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