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 (*metadata.txt):

Saving options in Micro-Manager
Micro-Manager saving option Micro-Manager saving format Companion file Bio-Formats reading Reader users
Save as separate image files TIFF Yes Full support MicromanagerReader
Save as image stack file OME-TIFF No Pixel data plus minimal 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: Tools ‣ Options… and then select “Create metadata.txt file with Image Stack Files” in the text box.