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1 | 1 | # Cytomine-python-client
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| -When using our software, we kindly ask you to cite our website url and related publications in all your work (publications, studies, oral presentations,...). In particular, we recommend to cite (Marée et al., Bioinformatics 2016) paper, and to use our logo when appropriate. See our license files for additional details. |
| 3 | +All data available from the Cytomine graphical interface can be manipulated programmatically from your computer. This page introduces the key concepts on how to interact with Cytomine without this graphical interface. Cytomine is a RESTful application. |
| 4 | +It means that the data stored and managed by Cytomine can be obtained through specific URLs. Contrary to the graphical interface, these URLs only provide relevant information data. |
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| -- URL: http://www.cytomine.org |
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| -- Logo: http://www.cytomine.org/sites/default/files/inline-images/logo-300-org.png |
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| -- Scientific paper: Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel. Collaborative analysis of multi-gigapixel imaging data using Cytomine, Bioinformatics, DOI: 10.1093/bioinformatics/btw013, 2016. https://doi.org/10.1093/bioinformatics/btw013 |
| 6 | +To ease interaction with Cytomine, the **Cytomine API client for Python** encapsulates all the technical details relative to the HTTP API so that you can manipulate Cytomine resources without complexity. |
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| 8 | +## Install |
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| -Cytomine (http://doc.cytomine.org) client and utilities in Python. |
| 10 | +``` |
| 11 | +pip install cytomine-python-client |
| 12 | +``` |
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| -Cytomine client contains functions to import/export data (projects, ontologies, images, users, annotations, softwares, ... ) from/to Cytomine core server based on the RESTful API. |
| 14 | +For versions lower than `2.3.4`, refer to [manual installation guide](https://doc.cytomine.com/dev-guide/clients/python/installation). |
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| -Cytomine utilities contains various functions including ones to access whole slide images (tiles, ...) and basic image processing tools. |
| 16 | +## Documentation |
| 17 | +* [How to interact with Cytomine programmatically introduction](https://doc.cytomine.com/dev-guide/api/) |
| 18 | +* [How to use the API client for Python](https://doc.cytomine.com/dev-guide/clients/python/usage) |
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| -See examples in https://github.com/cytomine/Cytomine-python-client/tree/master/client/examples and https://github.com/cytomine/Cytomine-python-client/tree/master/utilities/examples |
| 20 | +## Examples |
| 21 | +* [Detailed examples detailed step by step](https://doc.cytomine.com/dev-guide/clients/python/examples) |
| 22 | +* [Examples source code](https://github.com/cytomine/Cytomine-python-client/tree/master/client/examples) |
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| -The client is automatically installed with the Docker/Bootstrap procedure, however it is possible to install it independently on remote computers. See installation instructions here : [https://doc.cytomine.org/Python-client](https://doc.cytomine.org/Python-client?structure=DataScientists) |
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| 25 | +# More about Cytomine |
| 26 | +* [Cytomine Corporation SA](https://cytomine.com) |
| 27 | +* [Cytomine documentation](https://doc.cytomine.com) |
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