Added imageJ macro

MANIFEST.in

@@ -3,6 +3,7 @@ include README.md
 exclude .pre-commit-config.yaml
 
 recursive-include mesospim_stitcher *.py
+recursive-include mesospim_stitcher *.ijm
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

mesospim_stitcher/big_stitcher_bridge.py

@@ -0,0 +1,2 @@
+def run_big_stitcher():
+    return

mesospim_stitcher/stitch_macro.ijm

@@ -0,0 +1,19 @@
+run("Load TileConfiguration from File...",
+    "browse=D:/TiledDataset/2.5x_tile/2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv3.xml " +
+    "select=D:/TiledDataset/2.5x_tile//2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv3.xml " +
+    "tileconfiguration=D:/TiledDataset/2.5x_tile//2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv_tile_config.txt " +
+    "use_pixel_units keep_metadata_rotation");
+
+run("Calculate pairwise shifts ...",
+    "select=D:/TiledDataset/2.5x_tile//2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv3.xml " +
+    "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] " +
+    "process_tile=[All tiles] process_timepoint=[All Timepoints] " +
+    "method=[Phase Correlation] channels=[Average Channels] " +
+    "downsample_in_x=4 downsample_in_y=4 downsample_in_z=4");
+
+run("Optimize globally and apply shifts ...",
+    "select=D:/TiledDataset/2.5x_tile//2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv3.xml " +
+    "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] " +
+    "process_tile=[All tiles] process_timepoint=[All Timepoints] relative=2.500 absolute=3.500 " +
+    "global_optimization_strategy=[Two-Round using Metadata to align unconnected Tiles and iterative dropping of bad links] " +
+    "fix_group_0-0,");