Gallery
=====

.. _gallery:

Work in progress...

template
--------

.. only:: html

   .. figure:: _static/template.gif
A very simple model that has 1 cell type ("default") and 1 (unused) substrate ("substrate"). The number of initial cells (=5) are specified as a `User Parameter`. The simulation time is 5 days and results are output every hour. This cell type has a phenotype that includes:

* cell cycle resulting in proliferation
* cell death
* default adhesion and repulsion (mechanics)
* no motility
* no secretion


biorobots
---------

.. image:: ./gallery_imgs/biorobots0.png
   :width: 200px
.. image:: ./gallery_imgs/biorobots_12hr.png
   :width: 200px
.. image:: ./gallery_imgs/biorobots_2days.png
   :width: 200px
.. image:: ./gallery_imgs/biorobots_12hr_director_signal.png
   :width: 200px
.. image:: ./gallery_imgs/biorobots_12hr_cargo_signal.png
   :width: 200px

.. only:: html

   .. figure:: _static/biorobots.gif
* 3 cell/agent types: director, cargo, and worker
* 2 substrates (signals): director, cargo
* workers (red) pick up and deliver cargo (blue) to directors (green), using chemotaxis to signals

cancer biorobots
----------------

Similar to the biorobots sample, but now delivering a drug to treat a tumor. Therapy (cargo and worker cells) appears at 7 days, after the tumor has grown in size.

.. image:: ./gallery_imgs/cancerbots_6days.png
   :width: 200px
.. image:: ./gallery_imgs/cancerbots_7days.png
   :width: 200px
.. image:: ./gallery_imgs/cancerbots_8days.png
   :width: 200px
.. image:: ./gallery_imgs/cancerbots_10days.png
   :width: 300px
.. image:: ./gallery_imgs/cancerbots_userparams.png
   :width: 300px

.. only:: html

   .. figure:: _static/cancer_bots.gif
In the video, we are selecting different substrates to plot in the Studio.

* 3 cell types: cancer, cargo, and worker
* 3 substrates: oxygen, chemoattractant, therapeutic

heterogeneity
-------------

A growing tumor that experiences cell death as oxygen is depleted.
Cancer cells (from .svg output) are color-coded in C++. Live cells are green, but shaded by an oncoprotein value.
Apoptotic cells are red; necrotic are brown. Note in the images with 2 colorbars, the Studio can color cells' custom variables (scalars) with a continuous colormap, e.g., oncoprotein, using
the "full" (.mat, not .svg) output files.

.. image:: ./gallery_imgs/hetero_1hr.png
   :width: 200px
.. image:: ./gallery_imgs/hetero_10days.png
   :width: 200px
.. image:: ./gallery_imgs/hetero_15days.png
   :width: 200px
.. image:: ./gallery_imgs/hetero_27days.png
   :width: 500px
.. only:: html

   .. figure:: _static/hetero.gif
* 1 cell type: cancer
* 1 substrate: oxygen


virus-macrophage
----------------

Virus particles diffuse through the microenvironment, are uptaken by cells, replicate within cells, and trigger lytic death after reaching a threshold. Lysed cells release their virus particles to further diffuse through the environment. Macrophages move by random migration, test for contact with cells, and ingest / phagocytose cells based upon their viral load. Macrophages degrade their internalized viral particles.

.. image:: ./gallery_imgs/virus_mac_uptake.png
   :width: 500px
Showing the uptake rate of virus for epi cells.

.. image:: ./gallery_imgs/virus_mac_t0.png
   :width: 250px
.. image:: ./gallery_imgs/virus_mac_18hr.png
   :width: 250px
.. only:: html

   .. figure:: _static/virus_mac.gif
It goes fast, but part way through the video, we first plot the virus (substrate) then the interferon. 

* 2 cell types: epithelial cell, macrophage
* 2 substrates: virus, interferon

interaction
-----------

Complex interaction between multiple cell types and signals. Refer to the custom C++ phenotype functions https://github.com/MathCancer/PhysiCell/blob/master/sample_projects/interactions/custom_modules/custom.cpp

.. image:: ./gallery_imgs/interaction_t0.png
   :width: 400px
.. image:: ./gallery_imgs/interaction_cd8.png
   :width: 400px
.. only:: html

   .. figure:: _static/interaction.gif

* 7 cell types: bacteria, blood vessel, stem, differentiated, macrophage, CD8+ T cell, neutrophil
* 5 substrates: resource, toxin, quorum, pro-inflammatory, debris

worm
----

A sample project that shows advanced interaction testing and contact testing. (However, this functionality pre-dated the
ability to do so in XML, so it is all performed in custom.cpp).
Individual cells aggregate based on chemotaxis towards a secreted quorum factor and test for contacts. 
Cells can form a maximum of `n` (default: 2) attachments with the built-in spring functions. 
Cells on the ends (1 attachment) hold a steady expression of a differentiation function (`head`). 
This factor is exchanged between interior cells (2 attachments) to model juxtacrine signaling, using a contact function. 
End cells determine if they are a head or a tail based by comparing their expression with their linked neighbor. This introduces asymmmetry that allows the "worms" to crawl directionally. 
Cells exchange a differentiation factor across their contacts to model juxtacrine signaling. To help support contact interaction modeling, there are search functions to report a vector of Cells that are nearby for use in your contact interactions. The default mechanics function also records a list of all currently (mechanically) interacting cells in state.neighbors.

.. only:: html

  .. figure:: _static/worm.gif

* 1 cell type: worm
* 1 substrate: signal