.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/run_multi_fov_hcs_ome_zarr.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_run_multi_fov_hcs_ome_zarr.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_run_multi_fov_hcs_ome_zarr.py:


Multi-FOV HCS OME-Zarr
======================

This script writes a high content screening (HCS) OME-Zarr dataset
with a single FOV and a single scaling level per well,
and adds an extra well-position to an existing dataset.

.. GENERATED FROM PYTHON SOURCE LINES 11-19

.. code-block:: Python


    import os
    from tempfile import TemporaryDirectory

    import numpy as np

    from iohub.ngff import open_ome_zarr








.. GENERATED FROM PYTHON SOURCE LINES 20-21

Set storage path

.. GENERATED FROM PYTHON SOURCE LINES 21-26

.. code-block:: Python


    tmp_dir = TemporaryDirectory()
    store_path = os.path.join(tmp_dir.name, "hcs.zarr")
    print("Zarr store path", store_path)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Zarr store path /tmp/tmp5iaut2q0/hcs.zarr




.. GENERATED FROM PYTHON SOURCE LINES 27-32

Write 5D data to multiple wells.
Integer path names will be automatically converted to strings.
While the NGFF specification (and iohub) allows for arbitrary names,
the ome-zarr-py library and the napari-ome-zarr viewer
can only load positions and arrays with name '0' for the whole plate.

.. GENERATED FROM PYTHON SOURCE LINES 32-56

.. code-block:: Python


    position_list = (
        ("A", "1", "0"),
        ("H", 1, "0"),
        ("H", "12", "CannotVisualize"),
        ("Control", "Blank", 0),
    )

    with open_ome_zarr(
        store_path,
        layout="hcs",
        mode="w-",
        channel_names=["DAPI", "GFP", "Brightfield"],
    ) as dataset:
        # Create and write to positions
        # This affects the tile arrangement in visualization
        for row, col, fov in position_list:
            position = dataset.create_position(row, col, fov)
            position["0"] = np.random.randint(
                0, np.iinfo(np.uint16).max, size=(5, 3, 2, 32, 32), dtype=np.uint16
            )
        # Print dataset summary
        dataset.print_tree()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /
     ├── A
     │   └── 1
     │       └── 0
     │           └── 0 (5, 3, 2, 32, 32) uint16
     ├── Control
     │   └── Blank
     │       └── 0
     │           └── 0 (5, 3, 2, 32, 32) uint16
     └── H
         ├── 1
         │   └── 0
         │       └── 0 (5, 3, 2, 32, 32) uint16
         └── 12
             └── CannotVisualize
                 └── 0 (5, 3, 2, 32, 32) uint16




.. GENERATED FROM PYTHON SOURCE LINES 57-58

Append a channel to all the positions

.. GENERATED FROM PYTHON SOURCE LINES 58-68

.. code-block:: Python


    with open_ome_zarr(store_path, mode="r+") as dataset:
        for name, position in dataset.positions():
            print(f"Appending a channel to position: {name}")
            position.append_channel("Segmentation", resize_arrays=True)
            position["0"][:, 3] = np.random.randint(
                0, np.iinfo(np.uint16).max, size=(5, 2, 32, 32), dtype=np.uint16
            )
        dataset.print_tree()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Appending a channel to position: A/1/0
    Appending a channel to position: Control/Blank/0
    Appending a channel to position: H/1/0
    Appending a channel to position: H/12/CannotVisualize
    /
     ├── A
     │   └── 1
     │       └── 0
     │           └── 0 (5, 4, 2, 32, 32) uint16
     ├── Control
     │   └── Blank
     │       └── 0
     │           └── 0 (5, 4, 2, 32, 32) uint16
     └── H
         ├── 1
         │   └── 0
         │       └── 0 (5, 4, 2, 32, 32) uint16
         └── 12
             └── CannotVisualize
                 └── 0 (5, 4, 2, 32, 32) uint16




.. GENERATED FROM PYTHON SOURCE LINES 69-70

Try viewing the images with napari-ome-zarr

.. GENERATED FROM PYTHON SOURCE LINES 72-73

Clean up

.. GENERATED FROM PYTHON SOURCE LINES 73-74

.. code-block:: Python

    tmp_dir.cleanup()








.. _sphx_glr_download_auto_examples_run_multi_fov_hcs_ome_zarr.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: run_multi_fov_hcs_ome_zarr.ipynb <run_multi_fov_hcs_ome_zarr.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: run_multi_fov_hcs_ome_zarr.py <run_multi_fov_hcs_ome_zarr.py>`