.. _new-experiment-guide:

How to create a new experiment
------------------------------

This guide shows you how to create an experiment project and import your data. Learn more about the structure of an experiment project :doc:`here <data-organization>`.

Reference keys: :term:`experiment project`, :term:`well`, :term:`position`, :term:`cell population`, :term:`cell type`, :term:`antibody`, :term:`concentration`, :term:`pharmaceutical agents`

New project
~~~~~~~~~~~

#. Launch the software and go to **File > New Experiment...**

#. Set a folder where the project will be stored.

#. Fill in the requested fields (see :ref:`ref_experiment_config` for a full description of every parameter):

   Set the experiment name (no spaces), number of wells, positions per well,
   spatial and temporal calibrations, number of frames, movie prefix, and image
   dimensions.

    .. figure:: ../../_static/new_exp1.png
        :width: 60%
        :align: center
        :alt: static_class

        Fill requested information.

#. Select your channels and specify their index in the stack with the slider on the right side (0 is first, 1 is the second channel, etc). Use existing channels if appropriate. Else, create your own channel. Avoid spaces in the name.

#. Select your cell population(s). If you have an immune cell population, select ``effectors``. If you have cancer cells, select ``targets``. Else create appropriate populations:

    * Press the :icon:`plus,black` **Add a cell population** button.
    * Pick a name for the population: one word or camel case, no spaces, no special characters (e.g. `redBloodCells`, `macrophages`, `bacteria`).
    * Add. The population is added to the list of selectable populations. Check it to include it in the experiment.



    .. figure:: ../../_static/new_exp2.png
        :width: 60%
        :align: center
        :alt: static_class

        Example of a 5-channel and 3-population configuration.

#. Submit.

#. In the pop-up window, fill the information for each well (cell type, antibody, concentration, pharmaceutical agents). Fields can be left blank.

    .. figure:: ../../_static/new_exp3.png
        :width: 95%
        :align: center
        :alt: static_class

        Example for a 6-well experiment with multiple biological conditions.

#. After submitting:

   - The dialog closes.
   - The path to the newly created experiment is automatically loaded in the startup window. Click **Open** to access it.
   - On the disk, the experiment folder is created with a configuration file that looks like the example below.

Drag and drop the image stacks
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#. Open the project in Celldetective.  Click on the :icon:`folder,black` icon next to the experiment name in the top menu to open the experiment folder.

#. Drag and drop each TIF stack file in its its corresponding position folder, specifically in the ``movie/`` subfolder (e.g., ``W1/100/movie/``). Step **not automated**.