Update script

Author: schilling40

scripts/measurements/measure_synapses.py

@@ -11,9 +11,9 @@
 
 def check_project(plot=False, save_ihc_table=False, max_dist=None):
     s3 = create_s3_target()
-    cochleae = ['M_LR_000226_L', 'M_LR_000226_R', 'M_LR_000227_L', 'M_LR_000227_R']
-    synapse_table_name = "synapse_v3_ihc_v4"
-    ihc_table_name = "IHC_v4"
+    cochleae = ['M_LR_000226_L', 'M_LR_000226_R', 'M_LR_000227_L', 'M_LR_000227_R', 'M_AMD_OTOF1_L']
+    synapse_table_name = "synapse_v3_ihc_v4c"
+    ihc_table_name = "IHC_v4c"
 
     results = {}
     for cochlea in cochleae:

scripts/prediction/postprocess_ihc_synapse.py

@@ -4,8 +4,8 @@
 
 import imageio.v3 as imageio
 import pandas as pd
-import zarr
 from elf.io import open_file
+
 import flamingo_tools.segmentation.ihc_synapse_postprocessing as ihc_synapse_postprocessing
 from flamingo_tools.file_utils import read_image_data
 
@@ -63,9 +63,6 @@ def main():
 
     if args.tif:
         imageio.imwrite(args.out_path, output_, compression="zlib")
-    else:
-        with zarr.open(args.out_path, mode="a") as f_out:
-            f_out.create_dataset(args.out_key, data=output_, compression="gzip")
 
 
 if __name__ == "__main__":