openmicroscopy/bioformats — pull request #774 by tinevez (2013-10-30 15:57:22+00:00)
Title: A reader for the Yokagawa Cellvoyager automated microscope.

This reader opens the dataset generated by the Yokagawa Cellvoyager automated microscope.

The file format itself consists of several nested folder containing a lot of - sometimes redundant - information. This specific reader exploits the following files:
- MeasurementResult.xml that contains high level information about image geometry, well (if any) organization, fields arrangement, etc..
- MeasurementResult.ome.xml is a malformed OME xml file that contains information on one of the numerous TIF files that compose the pixel data. It is used to easily extract common metadata.
- all the TIF files in the Image folder: They contain the pixel data itself.

Each well (if any) can have several Areas (fields in the HCS vocable), in turn composed of several tiles that are to be stitched border to border, without the possibility of a more subtle stitching process. This reader stitches each area on the fly upon loading. It yields one series per well x area. If there is 20 wells each made of 2 areas, 40 series will be available,

This reader was built with the instrumental help of Melissa Linkert and Josh Moore.