diff --git a/SLURM_Snake_v2 b/SLURM_Snake_v2
index 4672b68..94cb0e6 100644
--- a/SLURM_Snake_v2
+++ b/SLURM_Snake_v2
@@ -41,7 +41,6 @@ snakemake \
     --cores $SLURM_NTASKS \
     --snakefile $SNAKEFILE \
     --use-singularity \
-    --use-conda \
     --directory $WORKDIR \
     --config list=$REAL_INPUTCSV
 
diff --git a/Scripts/Merge_files/Merge_files_main.py b/Scripts/Merge_files/Merge_files_main.py
old mode 100644
new mode 100755
diff --git a/Scripts/Morphology/Morphology_main.py b/Scripts/Morphology/Morphology_main.py
index d9051ff..691bbb7 100755
--- a/Scripts/Morphology/Morphology_main.py
+++ b/Scripts/Morphology/Morphology_main.py
@@ -18,7 +18,7 @@ def get_scale(metadata_file):
     data = json.load(f)
     first_value = list(data.values())[0]
 
-    if first_value['ruler']==True :
+    if first_value['has_ruler']==True :
 
         scale = round(first_value['scale'],3)
         unit = first_value['unit']
diff --git a/Snakefile b/Snakefile
index 03538fd..1479a6d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -50,7 +50,7 @@ rule Cropped_image:
     output:'Cropped/{image}_cropped.jpg'
     singularity:
         'docker://ghcr.io/hdr-bgnn/bgnn_snakemake/crop_morph:0.0.10'
-    shell: 'Crop_image_main.py.py {input.image} {input.metadata} {output}'
+    shell: 'Crop_image_main.py {input.image} {input.metadata} {output}'
 
 rule Segmentation:
     input: 'Cropped/{image}_cropped.jpg'
@@ -62,7 +62,7 @@ rule Segmentation:
 
 rule Morphological_analysis:
     input:
-        image = 'Segmented/{image}_segmented.png'
+        image = 'Segmented/{image}_segmented.png',
         metadata = 'Metadata/{image}.json'
         #name = '{image}'
     output: