Micro-Manager ============= `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 `_