.. empanada-napari-v1.1-dev documentation master file, created by
   sphinx-quickstart on Thu Feb  8 15:23:31 2024.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. _empanada-napari:

empanada-napari
=================

.. image:: _static/empanada-logo-new.gif
    :width: 1000px
    :height: 500px
    :align: center




.. grid:: 4
    :gutter: 2 2 4 4
    :padding: 4 4 0 0

    .. grid-item-card:: :octicon:`download` Getting Started
        :shadow: md

        Step-by-step **installation instructions** for the newest version for new or returning users
        +++

        .. button-ref:: getting_started
            :ref-type: ref
            :click-parent:
            :color: primary
            :expand:

            Getting Started

    .. grid-item-card:: :octicon:`image` Modules
        :shadow: md

        Detailed descriptions of parameters, outputs and demo videos of all the modules included in empanada-napari

        +++
        .. button-ref:: modules
            :ref-type: ref
            :click-parent:
            :color: primary
            :expand:

            Modules

    .. grid-item-card:: :octicon:`north-star` Tutorials
        :shadow: md

        Indepth tutorials on how to finetune, train and run inference through this plugin

        +++

        .. button-ref:: tutorials
            :ref-type: ref
            :click-parent:
            :color: primary
            :expand:

            Tutorials

    .. grid-item-card:: :octicon:`upload` Share your model
        :shadow: md

        Share your trained model with the us and the vEM community

        +++

        .. button-ref:: share-model
            :ref-type: ref
            :click-parent:
            :color: primary
            :expand:

            Share your model


This version of empanada-napari was created by Abhishek Bhardwaj and Madeline Barry `<https://cmm.ccr.cancer.gov/volume-em/>`_ :octicon:`link-external`

Citing this work
==================

If you use results generated by this plugin in a publication, please cite:

.. card::
   :link: https://www.cell.com/cell-systems/fulltext/S2405-4712(22)00494-X
   :width: 50%

   `Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model <https://www.cell.com/cell-systems/fulltext/S2405-4712(22)00494-X>`_ :octicon:`link-external`

   Conrad, R., & Narayan, K.

   (2023). Cell Systems, 14(1), 58-71. e5. //doi.org/10.1016/J.CELS.2022.12.006


.. toctree::
   :maxdepth: 2
   :hidden:

   Getting Started <getting_started/index>
   Modules <modules/index>
   Tutorials <tutorials/index>
   Best Practices <best_practice/index>
   FAQs <faq/index>