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macro:import_metamorph_screen_acquisition_tile_data
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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 13:13 (external edit)
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