====== Stitch data from MetaMorph 7 "Screen Acquisition" module ======
Reassembles tiling data acquired by MetaMorph into stacks and hyperstacks.

MetaMorph 7's Screen Acquisition (screenacq) does not natively support time and Z acquisitions from it's UI or journal functions.  Therefore it's easier to assemble the 5D experiment (x,y,z,t,c) with FIJI including stitch TIF files together with overlap.

=== Output ===
{{:macro:review_screen_data_output.png|Hyperstack output from running the "Stitch Raw Data" macro tool}}

=== Requirements ===
[[http://fiji.sc/wiki/index.php/Downloads|FIJI]], since this macro makes use of:
  * ImageJ 1.46c or later
  * [[http://fiji.sc/wiki/index.php/Image_Stitching|Grid/Collection stitching plugin]]

=== Installation ===
Download "Review Screen Data.txt" to the >Macros>Toolsets folder. It will show up in the ">>" toolsets dropdown under the name of the text file, "Review Screen Data".


^  Filename  ^  Last Modified  ^
|''{{:macro:rss:07a:review_screen_data.txt|Review Screen Data.txt}}''|  2013/02/04  |

=== License ===
Public Domain

=== Known Bugs ===
  - Window flicker for each well site while constructing hyperstack.
    * ImageJ has a bug where it throws a ''NullPointerException'' when using ''BatchMode'' to ''run("Stack to Hyperstack...", ...)'' followed by ''close()''.
    * As a workaround these functions need to be run outside of ''BatchMode'', which causes the ficker of the window appearing and closing.
    * Wayne Rasband is aware of this bug.
  - Crash during macro stitching leaves ''*.HTD'' metadata files renamed as ''*.HTD.bak''.
    * Re-run the macro to fix.
    * This renaming for is necessary to prevent the Bioformats reader from confusing MetaMorph ''*.HTD'' files to be Applied Precision files.

=== Change History ===
  * 2013.02.04 v0.7a
    * Fix "Stack required" error by skipping hyperstack assembly when not needed
  * 2013.02.03 v0.6
    * Fix for dot characters in dataset file naming
  * 2012.10.21 v0.5
    * Add Z projection macro
    * Add toolbar icons for multiple macros
    * Cleanup loop variables
  * 2012.10.18 v0.4
    * Fix single channel dataset file naming
  * 2012.10.15 v0.3
    * Initial public release
    * Add user input validation of Z slices
    * Workaround ImageJ BatchMode bug with creating hyperstack
    * Fix progress bar index
  * 2012.10.14 v0.2
    * Add progress bar
    * Add License
    * Create hyperstacks
  * 2012.10.12 v0.1
    * Initial development release

=== Future Additions / Improvements ===
  * LOCI tools Bioformats should add support for Molecular Devices ''*.HTD'' data.
  * Multi-well viewer macro to directly open a hyperstack by clicking the well position.