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macro:import_metamorph_screen_acquisition_tile_data

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macro:import_metamorph_screen_acquisition_tile_data [2019/04/12 11:13] (current)
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 +====== 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.
macro/import_metamorph_screen_acquisition_tile_data.txt ยท Last modified: 2019/04/12 11:13 (external edit)