.. _configuration:

Configuration files
=====================


Description of the configurations files:

Experimental metadata
---------------------

File description:
`Experimental metadata <https://github.com/linnarsson-lab/pysmFISH/blob/gh-pages/configuration_files/Experimental_metadata.yaml>`_


:download:`Experimental_metadata.yaml <Experimental_metadata.yaml>`


Filtering and raw counting
--------------------------

File description:
`Filtering and raw counting <https://github.com/linnarsson-lab/pysmFISH/blob/gh-pages/configuration_files/Filtering_raw_counting.config.yaml>`_


:download:`Filtering_raw_counting.config.yaml <Filtering_raw_counting.config.yaml>`



Staining segmentation
---------------------

File description:
`Staining segmentation <https://github.com/linnarsson-lab/pysmFISH/blob/gh-pages/configuration_files/Staining_segmentation.config.yaml>`_


:download:`Staining_segmentation.config.yaml <Staining_segmentation.config.yaml>`


Coordinate file:
----------------
This file containes the coordinates of the tiles forming the large area images.
The coords are exported from the raw nikon image files.

File description:
`Tile Coords <https://github.com/linnarsson-lab/pysmFISH/blob/gh-pages/configuration_files/Coords.txt>`_

:download:`Coords.txt <Coords.txt>`