Celldetective, a bioimage analysis software
===========================================

.. figure:: _static/logo.png
    :width: 300px
    :align: center
    :alt: logo

Celldetective offers both a **Python API** and a **Graphical User Interface (GUI)** to perform single-cell analysis on multimodal time-lapse microscopy images.


- `Check the source code <https://github.com/remyeltorro/celldetective>`_
- `Report a bug or request a new feature <https://github.com/remyeltorro/celldetective/issues/new/choose>`_
- `Explore the datasets models and demos <https://zenodo.org/records/10650279>`_


Check the :doc:`overview <overview>` for more general information or :doc:`get started <get-started>` with a detailed tutorial!

.. grid:: 2
    :gutter: 3

    .. grid-item-card:: :icon:`school` Tutorials
        :link: get-started
        :link-type: doc

        Step-by-step instructions to get you started with your first experiment.

    .. grid-item-card:: :icon:`text-box-check-outline` How-to Guides
        :link: how-to-guides/index
        :link-type: doc

        Recipe-like guides for specific tasks and advanced usage.

    .. grid-item-card:: :icon:`book-open-page-variant` Reference
        :link: reference/installation
        :link-type: doc

        Technical descriptions of installation, settings, file formats, and measurements.

    .. grid-item-card:: :icon:`lightbulb` Explanation
        :link: explanation_topics
        :link-type: doc

        High-level concepts and background information.


.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Tutorials:
   
   get-started
   first-experiment
   adcc-example
   example_notebook


.. toctree::
   :hidden:
   :maxdepth: 2
   :caption: How-to guides
   
   how-to-guides/index
   troubleshooting

.. toctree::
   :hidden:
   :maxdepth: 2
   :caption: Reference:

   reference/installation
   reference/settings
   reference/file-formats
   reference/menus
   reference/measurements
   reference/regionprops
   reference/glossary
   API

.. toctree::
   :hidden:
   :caption: Explanation:

   explanation_topics
   concepts

.. toctree::
   :hidden:
   :caption: About:

   acknowledegments
   cite
