Stains from ome-zarr, and Eed atlas labels

spimquant/config/snakebids.yml

@@ -1,4 +1,4 @@
-bids_dir: '/cifs/prado/Kate/AK_Pipeline_LSM/spimprep/bids/'
+bids_dir: '../tests/data'
 output_dir: '.'
 
 
@@ -23,8 +23,6 @@ pybids_inputs:
   spim:
     filters:
       suffix: 'SPIM'
-      #      acquisition: 4x #this will need to be blaze4x
-      subject: o28
       extension: 'ome.zarr'
     wildcards:
       - subject
@@ -46,7 +44,6 @@ parse_args:
     default: False
 
 
-
 #--- workflow specific configuration -- 
 
 
@@ -70,38 +67,59 @@ ome_zarr:
 
 template: ABAv3 #template to use
 
+
+
 templates:
   ABAv3:
     anat: '{workflow.basedir}/../resources/ABAv3/P56_Atlas.nii.gz'
     dseg: '{workflow.basedir}/../resources/ABAv3/P56_Annotation.nii.gz'
     lut: '{workflow.basedir}/../resources/ABAv3/labelmapper_ABAv3_to_all.json'
+    segs:
+      all: 
+        dseg: 'results/tpl-ABAv3/tpl-ABAv3_desc-LR_dseg.nii.gz'
+        tsv: 'results/tpl-ABAv3/tpl-ABAv3_desc-LR_dseg.tsv'
+      roi22: 
+        dseg: '{workflow.basedir}/../resources/ABAv3/eed_labels/P56_annotation_22_R_L.nii.gz'
+        csv: '{workflow.basedir}/../resources/ABAv3/eed_labels/P56_annotation_22_R_L.csv'
+      roi82:
+        dseg: '{workflow.basedir}/../resources/ABAv3/eed_labels/P56_annotation_82_R_L.nii.gz'
+        csv: '{workflow.basedir}/../resources/ABAv3/eed_labels/P56_annotation_82_R_L.csv'
+
+
   gubra:
     anat: '{workflow.basedir}/../resources/gubra/gubra_template_olf_affine_padABAv3.nii.gz'
     dseg: '{workflow.basedir}/../resources/gubra/gubra_ano_olf_affine_padABAv3_remap.nii.gz'
     lut: '{workflow.basedir}/../resources/ABAv3/labelmapper_ABAv3_to_all.json'
 
-stains:
+
+stains_for_reg: #ordered by priority
   - PI
+  - autof
+  - AutoF
+
+stains_for_blobdetect:
+  - abeta
+  - Abeta
   - BetaAmyloid
+  - AlphaSynuclein
 
+
 templatereg:
-  stain: PI #set this to PI for lifecanvas data 
   level: 5
   desc: N4brain
   zooms:
     #    - 20
     - 40
 
 masking:
-  stain: PI #set this to PI for lifecanvas data 
   level: 5
   priors_template: ABAv3
   gmm_k: 9
   gmm_bg_class: 1
   pre_atropos_downsampling: '50%'
 
 blobdetect:
-  level: 2 #downsampling level to use for blob detection
+  level: 4 #downsampling level to use for blob detection
   dseg_level: 5 # downsampling level to use for template when assigning labels to blobs
   dseg_template: ABAv3
-  stain: BetaAmyloid
+

spimquant/resources/ABAv3/eed_labels/P56_annotation_22_R_L.csv

@@ -0,0 +1,22 @@
+L_OLF,L_Olfactory areas,1
+R_OLF,R_Olfactory areas,2
+L_Iso,L_Isocortex,3
+R_ISO,R_Isocortex,4
+L_HYP,L_Hippocampal formation,5
+R_HYP,R_Hippocampal formation,6
+L_AMY,L_Amygdala,7
+R_AMY,R_Amygdala,8
+L_STR,L_Striatum,9
+R_STR,R_Striatum,10
+L_PAL,L_Pallidum,11
+R_PAL,R_Pallidum,12
+L_THA,L_Thalamus,13
+R_THA,R_Thalamus,14
+L_HY,L_Hypothalamus,15
+R_HY,R_Hypothalamus,16
+L_MB,L_Midbrain,17
+R_MB,R_Midbrain,18
+L_HB,L_Hindbrain,19
+R_HB,R_Hindbrain,20
+L_CEB,L_Cerebellum,21
+R_CEB,R_Cerebellum,22

spimquant/resources/ABAv3/eed_labels/P56_annotation_82_R_L.csv

@@ -0,0 +1,82 @@
+L_OLF,L_Olfactory_areas,1
+R_OLF,R_Olfactory_areas,2
+L_GU,L_Gustatory_areas,3
+R_GU,R_Gustatory_areas,4
+L_FRP,L_Frontal_pole_cerebral_cortex,5
+R_FRP,R_Frontal_pole_cerebral_cortex,6
+L_ECT,L_Ectorhinal_area,7
+R_ECT,R_Ectorhinal_area,8
+L_RSP,L_Retrosplenial_area,9
+R_RSP,R_Retrosplenial_area,10
+L_SS,L_Somatosensory_areas,11
+R_SS,R_Somatosensory_areas,12
+L_ILA,L_Infralimbic_area,13
+R_ILA,R_Infralimbic_area,14
+L_ACA,L_Anterior_cingulate_area,15
+R_ACA,R_Anterior_cingulate_area,16
+L_MO,L_Somatomotor_areas,17
+R_MO,R_Somatomotor_areas,18
+L_AI,L_Agranular_insular_area,19
+R_AI,R_Agranular_insular_area,20
+L_ORB,L_Orbital_area,21
+R_ORB,R_Orbital_area,22
+L_AUD,L_Auditory_areas,23
+R_AUD,R_Auditory_areas,24
+L_VISC,L_Visceral_area,25
+R_VISC,R_Visceral_area,26
+L_PERI,L_Perirhinal_area,27
+R_PERI,R_Perirhinal_area,28
+L_TEa,L_Temporal_association_areas,29
+R_TEa,R_Temporal_association_areas,30
+L_PTLp,L_Posterior_parietal_association_areas,31
+R_PTLp,R_Posterior_parietal_association_areas,32
+L_PL,L_Prelimbic_area,33
+R_PL,R_Prelimbic_area,34
+L_VIS,L_Visual_areas,35
+R_VIS,R_Visual_areas,36
+L_DG,L_Dentate_gyrus,37
+R_DG,R_Dentate_gyrus,38
+L_CA,L_Ammon's_horn,39
+R_CA,R_Ammon's_horn,40
+L_PAR,L_Parasubiculum,41
+R_PAR,R_Parasubiculum,42
+L_PRE,L_Presubiculum,43
+R_PRE,R_Presubiculum,44
+L_POST,L_Postsubiculum,45
+R_POST,R_Postsubiculum,46
+L_ProS,L_Prosubiculum,47
+R_ProS,R_Prosubiculum,48
+L_SUB,L_Subiculum,49
+R_SUB,R_Subiculum,50
+L_ENT,L_Entorhinal_area,51
+R_ENT,R_Entorhinal_area,52
+L_AMY,L_Amygdala,53
+R_AMY,R_Amygdala,54
+L_STRv,L_Striatum_ventral_region,55
+R_STRv,R_Striatum_ventral_region,56
+L_STRd,L_Striatum_dorsal_region,57
+R_STRd,R_Striatum_dorsal_region,58
+L_LSX,L_Lateral_septal_complex,59
+R_LSX,R_Lateral_septal_complex,60
+L_PAL,L_Pallidum,61
+R_PAL,R_Pallidum,62
+L_DORpm,L_Thalamus_polymodal_association_cortex_related,63
+R_DORpm,R_Thalamus_polymodal_association_cortex_related,64
+L_DORsm,L_Thalamus_sensory-motor_cortex_related,65
+R_DORsm,R_Thalamus_sensory-motor_cortex_related,66
+L_HY,L_Hypothalamus,67
+R_HY,R_Hypothalamus,68
+L_MBsen,L_Midbrain_sensory_related,69
+R_MBsen,R_Midbrain_sensory_related,70
+L_MBsta,L_Midbrain_behavioral_state_related,71
+R_MBsta,R_Midbrain_behavioral_state_related,72
+L_MBmot,L_Midbrain_motor_related,73
+R_MBmot,R_Midbrain_motor_related,74
+L_HB,L_Hindbrain,75
+R_HB,R_Hindbrain,76
+L_HEM,L_Hemispheric_regions,77
+R_HEM,R_Hemispheric_regions,78
+L_CBN,L_Cerebellar_nuclei,79
+R_CBN,R_Cerebellar_nuclei,80
+L_VERM,L_Vermal_regions,81
+R_VERM,R_Vermal_regions,82

spimquant/workflow/Snakefile

@@ -1,8 +1,5 @@
 from snakebids import bids, generate_inputs, get_wildcard_constraints, set_bids_spec
 from snakemake.utils import format
-import pathlib
-import os
-import shutil
 
 set_bids_spec("v0_11_0")
 
@@ -25,8 +22,28 @@ inputs = generate_inputs(
     participant_label=config.get("participant_label", None),
     exclude_participant_label=config.get("exclude_participant_label", None),
     validate=not config.get("plugins.validator.skip", False),
+#    ignore=["sourcedata"],  #this is needed to correct a bug when parsing pybids datasets with fsspec, but requires updated snakebids (in akhanf fork)
 )
 
+from lib.ome_zarr import get_channel_names
+
+# get stains from first subject (lazy - should use the correct stain for each subject, when defining target rules)
+stains = get_channel_names(inputs["spim"].expand()[0])
+print('stains in first subject:')
+print(stains)
+stain_for_reg = None
+for stain in config["stains_for_reg"]:
+    if stain in stains:
+        stain_for_reg = stain
+        break
+
+if stain_for_reg == None:
+    print("ERROR: a stain for registration was not found in the first OME zarr file")
+
+
+stains_for_blobdetect = list(
+    set(config["stains_for_blobdetect"]).intersection(set(stains))
+)
 root = "results"
 
 
@@ -52,23 +69,25 @@ rule all_templatereg_deform_zooms:
                 **inputs["spim"].wildcards
             ),
             template=config["template"],
-            stain=config["stains"],
+            stain=stains,
             res=config["templatereg"]["zooms"],
         ),
 
 
 rule all_blobdensity:
     input:
-        blob_density=inputs["spim"].expand(
+        inputs["spim"].expand(
             bids(
                 root=root,
                 datatype="micr",
+                seg="{seg}",
                 space="{template}",
                 stain="{stain}",
                 suffix="blobdensity.nii",
                 **inputs["spim"].wildcards
             ),
-            stain=config["blobdetect"]["stain"],
+            stain=stains_for_blobdetect,
+            seg=config["templates"][config["template"]]["segs"].keys(),
             template=config["template"],
         ),
 
@@ -83,7 +102,7 @@ rule all_blobs:
                 suffix="blobs.npy",
                 **inputs["spim"].wildcards
             ),
-            stain=config["stains"],
+            stain=stains_for_blobdetect,
         ),
 
 
@@ -100,7 +119,7 @@ rule all_templatereg_deform:
                 **inputs["spim"].wildcards
             ),
             template=config["template"],
-            stain=config["stains"],
+            stain=stains,
         ),
 
 
@@ -122,7 +141,8 @@ rule all_templatereg_lbl:
 rule all:
     default_target: True
     input:
-        rules.all_templatereg_deform.input,
+        rules.all_templatereg_deform_zooms.input,
+        rules.all_blobdensity.input,
 
 
 include: "rules/common.smk"

spimquant/workflow/lib/ome_zarr.py

@@ -0,0 +1,15 @@
+import zarr
+
+def get_channel_names(path):
+
+    group = zarr.open_group(path, mode='r')
+
+    # Access the .zattrs metadata as a dictionary
+    metadata = dict(group.attrs)
+
+    # Retrieve channel names
+    return [chan['label'] for chan in metadata['multiscales'][0]['metadata']['omero']['channels']]
+
+    return channel_names
+
+