# AO-LLSM

Code for supporting AO-LLSM analysis

Compilation: A CMakeLists.txt file is provided to compile the project using a C++ compiler. Use CMake and link to ITK libraries.

Tile stitching using TileReader.cxx. Name of binary: tileReader C++ Code stitches across 3D tiles and assembles any 5D region of interest. The code is multithreaded and parallelized.

Usage: $/tileReader iSettingsFile iTileDir oOutputImageDir Usage:

iSettings file directory -- Path of CSV file iTile directories - Path of individual image tiles oOutputImageDir - Stitched z plane directories

Options: -h --help Prints this help -b --blend Off Blends tiles at overlap -m --mip Off MIP of stitched tiles -c --channel 0 (default) channel value -t --time 0 (default) timepoint -s --zstart 0 (default) z start plane -e --zend 100 (default) z end plane -n --threads 1 (default) number of threads -l --lsMap (default) correction filename -d --darkLevel 30 (default) correction threshold -v --var 2.0 (default) smoothing scale -x --exp _ch (default) string marking channel information -d --deconv ~/ (default) deconvolve tiles based on PSF -p --sxy 1 (default) subsampling rate in X/Y -q --sz 1 (default) subsampling rate in Z -o --offset ~/ (default) offset filename

Tile registration using TileRegistration.cxx. Name of binary: tileRegistration Usage: iSettings file directory -- Path of CSV file iTile directories - Path of individual image tiles oOutputImageDir - Stitched z plane directories

iSettings file directory iTile directories

-h --help Prints this help -c --channel 0 (default) channel value -t --time 0 (default) timepoint -n --threads 1 (default) number of threads -x --exp _ch (default) string marking channel information -o --offset ~/ (default) offset filename -r --reg Off (default) register z tiles -s --zstart 0 (default) z tile

Convert image formats using ConvertFormat.cxx Usage: ./convertFormat iInputSettingsFile iInputImageDir iChannelNumber iTimePoint oOutputImageDir

Deconvolve brightfield images using Deconvolution.cxx Usage: ./deconvolve iInputImage iKernelImage oOutputImage numOfIterations

Maximum Projection using MaxProjection.cxx Usage: ./maxProj iInputFile oOutputFile

Extract region of interest in a timelapse dataset Usage: ./roiExtract input output