Restructured docs toc

docs/html/index.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 .. raw:: html
 
     <meta http-equiv="refresh" content="0; url=https://mannlabs.github.io/scPortrait/index.html">

docs/index.rst

@@ -16,7 +16,7 @@ Check out the installation instructions :ref:`here<installation>`. You can valid
 Getting Started
 ===============
 
-You can check out our :ref:`quickstart<quickstart>` guide to get started with scPortrait. For more detailed information on the package, we have written an in depth :ref:`computational workflow <pipeline>` guide. In the github repository you can also find some `tutorial notebooks <https://github.com/MannLabs/scPortrait/tree/main/docs_source/pages/notebooks>`_ as well as `small example datasets <https://github.com/MannLabs/SPARCSspatial/tree/main/example_data>`_ to get started with. If you encounter issues feel free to `open up a git issue <https://github.com/MannLabs/scPortrait/issues>`_.
+You can check out our :ref:`introduction<introduction>` to get started with scPortrait. For more detailed information on the package, we have written an in depth :ref:`computational workflow <pipeline>` guide. In the github repository you can also find some `tutorial notebooks <https://github.com/MannLabs/scPortrait/tree/main/docs_source/pages/notebooks>`_ as well as `small example datasets <https://github.com/MannLabs/SPARCSspatial/tree/main/example_data>`_ to get started with. If you encounter issues feel free to `open up a git issue <https://github.com/MannLabs/scPortrait/issues>`_.
 
 Citing our Work
 ================
@@ -41,7 +41,8 @@ Documentation
    :maxdepth: 2
    :caption: Ecosystem
 
-   pages/quickstart/
+   pages/installation/
+   pages/introduction/
    pages/pipeline/
    pages/tutorials
 

docs/pages/quickstart/introduction.rst → docs/pages/introduction.rst

@@ -4,7 +4,7 @@
 Introduction
 ************
 
-.. image:: ../images/scPortrait_workflow_steps.png
+.. image:: images/scportrait_workflow_steps.png
    :width: 100%
    :align: center
    :alt: scPortrait workflow steps: Segmentation, Extraction, Classification, Selection
@@ -37,13 +37,13 @@ Segmentation
 
 The cell segmentation process in scPortrait is split into two parts: **nuclear segmentation**, which identifies nuclei in the input image, and **cytoplasmic segmentation**, which identifies cytosols. Depending on the dataset and/or application it is possible that only one of the two segmentation types is required. In this case, the segmentation process can be configured to only perform a nuclear or a cytoplasmic segmentation.
 
-.. |pic1| image:: ../images/input_image.png
+.. |pic1| image:: images/input_image.png
    :width: 100%
 
-.. |pic2| image:: ../images/nucleus_mask.png
+.. |pic2| image:: images/nucleus_mask.png
    :width: 100%
 
-.. |pic3| image:: ../images/cytosol_mask.png
+.. |pic3| image:: images/cytosol_mask.png
    :width: 100%
 
 +-----------------------+-----------------------+-----------------------+
@@ -56,10 +56,10 @@ During the segmentation process, a mask is generated which maps the pixels of th
 
 If we zoomed in on the corner of the segmentation mask of a nucleus, the segmentation mask (a numpy array) would look like this:
 
-.. |pic4| image:: ../images/nucleus_mask_excerpt.png
+.. |pic4| image:: images/nucleus_mask_excerpt.png
    :width: 100%
 
-.. |pic5| image:: ../images/nucleus_mask_numeric.png
+.. |pic5| image:: images/nucleus_mask_numeric.png
    :width: 100%
 
 +-----------------------+-----------------------+
@@ -77,7 +77,7 @@ Extraction
 
 The scPortrait framework is built around the idea of generating standardized single-cell image datasets. A scPortrait single cell image dataset consists of a collection of images for each cell, containing both the segmentation masks and imaging channels of that particular cell. Aggregated across all cells in a scPortrait dataset, these image collections are saved as ``HDF5``, a container file format that enables the retrieval of individual cells without loading the entire dataset. These ``HDF5`` datasets are created during the extraction step.
 
-.. image:: ../images/single_cell_dataset.png
+.. image:: images/single_cell_dataset.png
    :width: 100%
    :align: center
    :alt: scPortrait single cell image dataset example