Update processing scripts

Author: constantinpape

flamingo_tools/data_conversion.py

@@ -10,7 +10,11 @@
 import numpy as np
 import pybdv
 
-from cluster_tools.utils.volume_utils import write_format_metadata
+try:
+    from cluster_tools.utils.volume_utils import write_format_metadata
+except ImportError:
+    write_format_metadata = None
+
 from elf.io import open_file
 from skimage.transform import rescale
 

reproducibility/templates_processing/REAMDE.md

@@ -12,6 +12,7 @@ For IHC segmentation run:
 - apply_unet_IHC_template.sbatch
 - segment_unet_IHC_template.sbatch
 
-For ribbon synapse detection run:
-- detect_synapse_marker_template.sbatch
+For ribbon synapse detection without associated IHC segmentation run
 - detect_synapse_template.sbatch
+For ribbon synapse detection with associated IHC segmentation run
+- detect_synapse_marker_template.sbatch

reproducibility/templates_processing/apply_unet_IHC_template.sbatch

@@ -9,7 +9,8 @@
 #SBATCH -a 0-9
 
 source ~/.bashrc
-micromamba activate micro-sam_gpu
+# micromamba activate micro-sam_gpu
+micromamba activate sam
 
 # Print out some info.
 echo "Submitting job with sbatch from directory: ${SLURM_SUBMIT_DIR}"
@@ -19,7 +20,8 @@ echo "Current node: ${SLURM_NODELIST}"
 
 # Run the script
 
-SCRIPT_REPO=/user/schilling40/u15000/flamingo-tools
+# SCRIPT_REPO=/user/schilling40/u15000/flamingo-tools
+SCRIPT_REPO=/user/pape41/u12086/Work/my_projects/flamingo-tools
 cd "$SCRIPT_REPO"/flamingo_tools/segmentation/ || exit
 
 export SCRIPT_DIR=$SCRIPT_REPO/scripts
@@ -37,7 +39,8 @@ export INPUT=/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/"$COC
 
 export OUTPUT_FOLDER=/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/predictions/"$COCHLEA"/"$SEG_NAME"
 
-export MODEL=/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/trained_models/IHC/v4_cochlea_distance_unet_IHC_supervised_2025-07-14
+# export MODEL=/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/trained_models/IHC/v4_cochlea_distance_unet_IHC_supervised_2025-07-14
+export MODEL=/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/trained_models/IHC/v5_cochlea_distance_unet_IHC_supervised_2025-08-20/
 export PREDICTION_INSTANCES=10
 export INPUT_KEY="setup$STAIN_CHANNEL/timepoint0/s0"
 

reproducibility/templates_processing/mean_std_IHC_template.sbatch

@@ -8,11 +8,13 @@
 #SBATCH --mem 128G
 
 source ~/.bashrc
-micromamba activate flamingo13
+# micromamba activate flamingo13
+micromamba activate sam
 
 # Run the script
 
-SCRIPT_REPO=/user/schilling40/u15000/flamingo-tools
+# SCRIPT_REPO=/user/schilling40/u15000/flamingo-tools
+SCRIPT_REPO=/user/pape41/u12086/Work/my_projects/flamingo-tools
 cd "$SCRIPT_REPO"/flamingo_tools/segmentation/ || exit
 
 export SCRIPT_DIR=$SCRIPT_REPO/scripts

reproducibility/templates_processing/segment_unet_IHC_template.sbatch

@@ -1,10 +1,10 @@
 #!/bin/bash
 #SBATCH --job-name=segment-unet-SGN
-#SBATCH --time 10:00:00             # for gerbil up to ~30 hours
+#SBATCH --time 35:00:00             # for gerbil up to ~30 hours
 
 #SBATCH -p standard96s:shared         # the partition
 #SBATCH -A nim00007
-#SBATCH -c 8
+#SBATCH -c 12
 #SBATCH --mem 400G
 
 source ~/.bashrc