# Macro Collection for BigStitcher Automation by Stephan Janosch, janosch@mpi-cbg.de, https://orcid.org/0000-0002-2401-6862 DOI for this software: https://doi.org/10.17617/1.6L First you run ***stich_a_day*** on a folder with daily recordings. This takes a while. Second you run fix filenames somewhere in output folder. This fixes the filename (which takes a long time) and generates quickview jpgs. ## stitch_a_day 2 macros for stitching: - a directory hierarchie full of - tifs, each containing multiple channels and tiles Indicate files for stitiching via ***_stitch_*** or any other substring 1 macro for just doing a fusion for all xmls in a daily recording folder. ### MacOs A directory naming convention like this works ``` /Volumes/SarovHFSP/2018-09-18 SD1 Andre/TRG_1678/ ``` ``` TRG_1678_16C_to_25C_TimelapseZ_0.tif TRG_1678_@16C_stitch_1.tif TRG_1678_16C_to_25C_timelapseZ_1.tif TRG_1678_@16C_stitch_2.tif TRG_1678_@16C_stitch_0.tif TRG_1678_@28C_stitch_0.tif ``` ### Windows map network drive. Have the days folders in the root of the drive ``` Z:\2018-09-18 SD1 Andre\TRG_1678\ ``` ### stitch_a_day_macos.ijm Does the whole pipeline on mac ### stitch_a_day_windows.ijm Does the pipeline on windows ### stitch_a_day_windows_fusion_only1x.ijm Does only the fusion for a daily recording folder ### fix_filenames_and_create_quickview.ijm Fixes all filenames for suffixed-output files. Directory needed to be created via a script above. Select at least one folder above your fused_tp0_ch0* files. Will traverse a whole directory structure. This script will not recreate JPGs, so you have to delete them before hand. ```bash find -name "*jpg" -delete ```