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

Hyperstack output from running the "Stitch Raw Data" macro tool

Requirements

FIJI, since this macro makes use of:

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
Review Screen Data.txt 2013/02/04

License

Public Domain

Known Bugs

  1. 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.
  2. 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.
macro/import_metamorph_screen_acquisition_tile_data.txt · Last modified: 2013/02/05 05:00 by omsai
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