.. _`assign_blastema_region`:
========================================
Detect blastema by pigment difference
========================================

Workflow
---------------------------------

.. image:: ../_static/assign_blastema_region_workflow.png
    :alt: Title figure
    :width: 700px
    :align: center

Example
---------------------------------


raw photo
++++++++++++++++++++++++++++++++++++

.. image:: ../_static/assign_blastema_region_raw.png
    :alt: Title figure
    :width: 350px
    :align: center

2D mapping photo of 3D atlas
++++++++++++++++++++++++++++++++++++

.. image:: ../_static/assign_blastema_region_2d.png
    :alt: Title figure
    :width: 350px
    :align: center

align photo and detect wound mask
++++++++++++++++++++++++++++++++++++

.. image:: ../_static/assign_blastema_region_aligned.png
    :alt: Title figure
    :width: 700px
    :align: center

assign region to each cell
++++++++++++++++++++++++++++++++++++

.. code-block:: python3

    python3 BlastemaByWound_v2.py

===================== ================================================================================================
arguments             description
===================== ================================================================================================   
-p                    prefix
-o                    output prefix, default output
-e                    exponential number, default 2
--only_wound          yes/no, default no
-l                    left wound left extern distance, default 20
--lr                  left wound right extern distance, default 20
--rl                  right wound left extern distance, default 20
--rr                  right wound right extern distance, default 20
===================== ================================================================================================   

Note: the unit of distance is 3 micron, so the default 10 refer to 60 microns.

Example :

- example 01: python3 BlastemaByWound.py -p 12hpa1

- example 02: python3 BlastemaByWound.py -p WT -o test_WT

- example 02: python3 BlastemaByWound.py -p 5dpa1 -o test_5dpa1 -e 3

- example 03: python3 BlastemaByWound.py -p 3dpa1 -o test_3dpa1_lr15 --lr 15

Output label :

- 1 -- [red]     left blastema

- 2 -- [green]   left margin of left wound

- 3 -- [magenta] right margin of left wound

- 4 -- [yellow]  body

- 5 -- [white]   left margin of right wound

- 6 -- [cyan]    right margin of right wound

- 7 -- [orange]  right blastema

Output label in only_wound mode:

- 3 -- [magenta] left wound region, similar to 1+2+3 in blastema mode

- 4 -- [yellow]  body

- 5 -- [white]   right wound region, similar to 5+6+7 in blastema mode


final region image
++++++++++++++++++++++++++++++++++++

.. image:: ../_static/assign_blastema_region_final.png
    :alt: Title figure
    :width: 350px
    :align: center