Micro-Manager
=============

`Micro-Manager <https://www.micro-manager.org/wiki/Micro-Manager>`_ is a
software framework for implementing advanced and novel imaging procedures,
extending functionality, customization and rapid development of specialized
imaging applications.

Micro-Manager offers the functionality for saving the acquired images in
TIFF/OME-TIFF format. Based on the mode of saving and the configuration
settings, the acquired image can be saved with or without a companion file
(:file:`*metadata.txt`):

.. figure:: /images/micromanager_saving.png
    :width: 50%
    :align: center
    :alt: Saving options in Micro-Manager


+---------------+----------+--------------+--------------+--------------------+
|Saving         |          |              |              |                    | 
|Options within |          |Companion     |Bio-Formats   |                    |
|Micro-Manager  |Format    |File          |Reading       | Reader Used        |
+===============+==========+==============+==============+====================+ 
| Save as       |          |              |              |                    |
| separate      |          |              |              |                    | 
| image files   | TIFF     | Yes          | Full Support | MicromanagerReader |
+---------------+----------+--------------+--------------+--------------------+ 
|               |          |              | Pixel data   |                    |
|               |          |              | plus minimal |                    |
|               | OME-TIFF | No           | metadata*    | OMETiffReader      |
| Save as image +----------+--------------+--------------+--------------------+
| stack file    |          |              |              |                    |
|               | OME-TIFF | Yes**        | Full Support | MicromanagerReader |
+---------------+----------+--------------+--------------+--------------------+ 


``*`` Not all acquisition metadata is converted to OME-XML.

``**`` A small change in the acquisition side facilitates better handling of
the metadata from the Bio-Formats side:
:menuselection:`Tools --> Options...` and then select "Create metadata.txt
file with Image Stack Files" in the text box.

.. seealso:: `Micro-Manager User's Guide - Files on Disk <https://micro-manager.org/wiki/Micro-Manager_User%27s_Guide#Files_on_Disk>`_