Merge pull request #143 from khanlab/coloc-resources

resource updates for coloc run

Author: akhanf

spimquant/config/snakebids.yml

@@ -63,35 +63,12 @@ parse_args:
      - MBMv3
      - turone
 
-  --template_mri:
-    help: "Template to use for MRI registration to obtain brain mask\n"
-    default: MouseIn
-    choices:
-      - MouseIn
-      - DSURQE
-      - MBMv3
-      - turone
-
   --atlas_segs:
-    help: "Atlas segmentations to use with the chosen template (default: use them all)"
+    help: "Atlas segmentations to use with the chosen template (default: predefined list or all)"
     default: null
     action: store
     nargs: '+'
 
-  --patch_atlas_segs:
-    help: "Atlas segmentations to use for extracting patches (default: roi22)"
-    default:
-      - roi22
-    action: store
-    nargs: '+'
-
-
-
-  --template_negative_mask:
-    help: "Negative mask, in the template space, to highlight regions to avoid\n"
-    type: Path
-    default: placeholder
-
   --template_crop:
     help: "Crop template along X-axis to retain specific hemisphere for registration (default: %(default)s)"
     choices: 
@@ -105,13 +82,14 @@ parse_args:
       - PI
       - YOPRO
       - YoPro
+      - YoPro1
       - AutoF
       - autof
     action: store
     nargs: '+'
 
   --stains_for_seg:
-    help: "List of stains to use for segmentation and quantification\n (default: %(default)s)"
+    help: "List of stains to use for segmentation and quantification (will segment any that match the data)\n (default: %(default)s)"
     default: 
       - abeta
       - Abeta
@@ -123,19 +101,21 @@ parse_args:
     nargs: '+'
 
   --stains_for_vessels:
-    help: "List of stains to use for vessel segmentation and quantification\n (default: %(default)s)"
+    help: "List of stains to use for vessel segmentation and quantification (will choose first available, in order)\n (default: %(default)s)"
     default: 
       - CD31
       - Lectin
     action: store
     nargs: '+'
 
   --registration_level:
-    help: "Downsampling level to use for registration (level 0 is full res, level 1 is 50% size, ...) (default: %(default)s)"
+    help: "Downsampling level to use for registration (level 0 is full res, level 1 is 50% size, ...) (default: 5)"
+    type: int
     default: 5
 
   --segmentation_level:
-    help: "Downsampling level to use for segmentation (level 0 is full res, level 1 is 50% size, ...) (default: %(default)s)"
+    help: "Downsampling level to use for segmentation (including vessels) (level 0 is full res, level 1 is 50% size, ...) (default: 0)"
+    type: int
     default: 0
 
   --no_segmentation:
@@ -179,6 +159,15 @@ parse_args:
     action: store_true
     default: False
 
+  --template_mri:
+    help: "Template to use for MRI registration to obtain brain mask\n"
+    default: MouseIn
+    choices:
+      - MouseIn
+      - DSURQE
+      - MBMv3
+      - turone
+
   --mri_resample_percent:
     help: "Resampling factor for multi-MRI averaging to create super-resolved images, as a percent (default: %(default)s). Use 200 for upsampling to twice the resolution"
     default: 100
@@ -219,6 +208,14 @@ parse_args:
     nargs: 3
     type: int
 
+  --patch_atlas_segs:
+    help: "Atlas segmentations to use for extracting patches (default: coarse)"
+    default:
+      - coarse
+    action: store
+    nargs: '+'
+
+
   --n_patches_per_label:
     help: "Number of patches to extract per atlas label (default: %(default)s)"
     default: 5
@@ -240,11 +237,12 @@ parse_args:
     nargs: '+'
 
   --crop_atlas_segs:
-    help: "Atlas segmentations to use for extracting Imaris crops (default: roi22)"
+    help: "Atlas segmentations to use for extracting Imaris crops (default: coarse)"
     default:
-      - roi22
+      - coarse
     action: store
     nargs: '+'
+
   --contrast_column:
     help: "Column name in participants.tsv to use for defining group contrasts (e.g., 'treatment', 'genotype'). Required for group-level statistical analysis."
     default: null

spimquant/workflow/Snakefile

@@ -11,7 +11,7 @@ tpl_spec = spec[0].copy()
 tpl_spec["entity"] = "template"
 tpl_spec["tag"] = "tpl"
 spec.insert(0, tpl_spec)
-snakebids.set_bids_spec(spec)
+set_bids_spec(spec)
 
 
 configfile: "config/snakebids.yml"

spimquant/workflow/rules/counts.smk

@@ -90,7 +90,7 @@ rule coloc_per_voxel_template:
         ),
     threads: 16
     resources:
-        mem_mb=15000,
+        mem_mb=64000,
         runtime=30,
     script:
         "../scripts/coloc_per_voxel_template.py"

spimquant/workflow/rules/regionprops.smk

@@ -134,10 +134,10 @@ rule colocalize_regionprops:
             suffix="coloc.parquet",
             **inputs["spim"].wildcards,
         ),
-    threads: 1
+    threads: 16
     resources:
-        mem_mb=1500,
-        runtime=30,
+        mem_mb=64000,
+        runtime=180,
     script:
         "../scripts/compute_colocalization.py"
 
@@ -180,9 +180,9 @@ rule sample_at_vessel_sdt:
             suffix="regionprops.parquet",
             **inputs["spim"].wildcards,
         ),
-    threads: 1
+    threads: 8
     resources:
         mem_mb=32000,
-        runtime=30,
+        runtime=360,
     script:
         "../scripts/sample_at_points.py"

spimquant/workflow/rules/segmentation.smk

@@ -236,38 +236,3 @@ rule clean_segmentation:
         runtime=30,
     script:
         "../scripts/clean_segmentation.py"
-
-
-rule deform_negative_mask_to_subject_nii:
-    input:
-        ref=bids(
-            root=root,
-            datatype="micr",
-            stain=stain_for_reg,
-            level="{level}",
-            suffix="SPIM.nii.gz",
-            **inputs["spim"].wildcards,
-        ),
-        mask=config["template_negative_mask"],
-        xfm_composite_inv=rules.compose_subject_to_template_warp.output.xfm_composite_inv,
-    output:
-        mask=bids(
-            root=root,
-            datatype="seg",
-            desc="negative",
-            level="{level}",
-            from_="{template}",
-            suffix="mask.nii.gz",
-            **inputs["spim"].wildcards,
-        ),
-    threads: 32
-    resources:
-        mem_mb=1500,
-        runtime=15,
-    conda:
-        "../envs/ants.yaml"
-    shell:
-        "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
-        "antsApplyTransforms -d 3 -v -n NearestNeighbor "
-        " -i {input.mask} -o {output.mask} "
-        " -r {input.ref} -t {input.xfm_composite_inv}"

spimquant/workflow/rules/segstats.smk

@@ -39,9 +39,9 @@ rule map_regionprops_to_atlas_rois:
                 **inputs["spim"].wildcards,
             )
         ),
-    threads: 1
+    threads: 4
     resources:
-        mem_mb=1500,
+        mem_mb=32000,
         runtime=15,
     script:
         "../scripts/map_atlas_to_regionprops.py"
@@ -84,9 +84,9 @@ rule map_coloc_to_atlas_rois:
                 **inputs["spim"].wildcards,
             )
         ),
-    threads: 1
+    threads: 4
     resources:
-        mem_mb=1500,
+        mem_mb=32000,
         runtime=15,
     script:
         "../scripts/map_atlas_to_coloc.py"