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# Macro Collection for BigStitcher Automation

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by Stephan Janosch, janosch@mpi-cbg.de, https://orcid.org/0000-0002-2401-6862

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DOI for this software: https://doi.org/10.17617/1.6L

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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.


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## stitch_a_day

2 macros for stitching:
- a directory hierarchie full of
- tifs, each containing multiple channels and tiles
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Indicate files for stitiching via ***_stitch_*** or any other substring

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1 macro for just doing a fusion for all xmls in a daily recording folder. 

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### 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

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map network drive. Have the days folders in the root of the drive

```
Z:\2018-09-18 SD1 Andre\TRG_1678\
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```

### 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

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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 <folder> -name "*jpg" -delete
```