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clean up target rules, check stains for all subjects #92

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Merged
akhanf merged 6 commits into from
Dec 19, 2025
Merged

clean up target rules, check stains for all subjects #92

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25a28ae
clean up target rules, check stains for all subjects
akhanf Dec 19, 2025
0567b37
Update spimquant/workflow/Snakefile
akhanf Dec 19, 2025
4bfc13f
Update spimquant/workflow/Snakefile
akhanf Dec 19, 2025
8c01944
Initial plan
Copilot Dec 19, 2025
249696c
Replace == None with is None for PEP 8 compliance
Copilot Dec 19, 2025
ec0c2e2
Merge pull request #93 from khanlab/copilot/sub-pr-92
akhanf Dec 19, 2025
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4 changes: 2 additions & 2 deletions spimquant/config/snakebids.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@ analysis_levels: &analysis_levels
#mapping from analysis_level to set of target rules or files
targets_by_analysis_level:
participant:
- '' # if '', then the first rule is run
- 'all_participant' # if '', then the first rule is run
group:
- 'all_group_stats'
- 'all_group'

# Configure components:
# Each entry creates a new component that can be retreived within the workflow
Expand Down
164 changes: 90 additions & 74 deletions spimquant/workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -30,27 +30,29 @@ inputs = generate_inputs(
)


# get stains from first subject (lazy - should use the correct stain for each subject, when defining target rules)
# to do this, would need to get the channel names in the function that gets the target rules
stains = ZarrNii.from_ome_zarr(inputs["spim"].expand()[0]).list_channels()
include: "rules/common.smk"


stains = get_stains_all_subjects()

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:
raise ValueError(
"a stain for registration was not found in the first OME zarr file"
)
if stain_for_reg is None:
raise ValueError(f"a stain for registration was not found in {stains}")


stains_for_seg = list(set(config["stains_for_seg"]).intersection(set(stains)))

do_coloc = len(stains_for_seg) > 1

# atlas segmentations to use
all_atlas_segs = config["templates"][config["template"]]["atlases"].keys()

if config["atlas_segs"] == None:
if config["atlas_segs"] is None:
atlas_segs = all_atlas_segs
else:
atlas_segs = []
Expand Down Expand Up @@ -106,7 +108,7 @@ rule all_templatereg_deform_zooms:
space="{template}",
stain="{stain}",
res="{res}um",
suffix="SPIM.nii",
suffix="SPIM.nii.gz",
**inputs["spim"].wildcards,
),
template=config["template"],
Expand All @@ -124,7 +126,7 @@ rule all_templatereg_deform:
desc="deform",
space="{template}",
stain="{stain}",
suffix="SPIM.nii",
suffix="SPIM.nii.gz",
**inputs["spim"].wildcards,
),
template=config["template"],
Expand Down Expand Up @@ -156,7 +158,7 @@ rule all_fieldfrac_tune:
stain="{stain}",
level="{level}",
desc="otsu+k{k}i{i}",
suffix="fieldfrac.nii",
suffix="fieldfrac.nii.gz",
**inputs["spim"].wildcards,
),
stain=stains_for_seg,
Expand All @@ -175,7 +177,7 @@ rule all_segment:
seg="{seg}",
space="{template}",
desc="{desc}",
suffix="{stain}+{suffix}.nii",
suffix="{stain}+{suffix}.nii.gz",
**inputs["spim"].wildcards,
),
seg=atlas_segs,
Expand All @@ -184,29 +186,14 @@ rule all_segment:
suffix=config["seg_metrics"],
stain=stains_for_seg,
),
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
seg="{seg}",
space="{template}",
desc="{desc}",
suffix="coloc+{suffix}.nii",
**inputs["spim"].wildcards,
),
seg=atlas_segs,
desc=config["seg_method"],
template=config["template"],
suffix=config["coloc_seg_metrics"],
),
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
stain="{stain}",
level="{level}",
space="{template}",
suffix="SPIM.nii",
suffix="SPIM.nii.gz",
**inputs["spim"].wildcards,
),
stain=stains_for_seg + [stain_for_reg],
Expand All @@ -221,7 +208,7 @@ rule all_segment:
level="{level}",
desc="{desc}",
space="{template}",
suffix="fieldfrac.nii",
suffix="fieldfrac.nii.gz",
**inputs["spim"].wildcards,
),
stain=stains_for_seg,
Expand Down Expand Up @@ -254,7 +241,7 @@ rule all_segment:
stain="{stain}",
level="{level}",
desc="{desc}",
suffix="counts.nii",
suffix="counts.nii.gz",
**inputs["spim"].wildcards,
),
stain=stains_for_seg,
Expand All @@ -268,7 +255,7 @@ rule all_segment:
stain="{stain}",
space="{template}",
desc="{desc}",
suffix="counts.nii",
suffix="counts.nii.gz",
**inputs["spim"].wildcards,
),
stain=stains_for_seg,
Expand All @@ -279,24 +266,43 @@ rule all_segment:
bids(
root=root,
datatype="micr",
desc="{desc}",
stain="{stain}",
space="{template}",
suffix="regqc.html",
**inputs["spim"].wildcards,
),
stain=stain_for_reg,
template=config["template"],
),


rule all_segment_coloc:
input:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
seg="{seg}",
space="{template}",
suffix="coloccounts.nii",
desc="{desc}",
suffix="coloc+{suffix}.nii.gz",
**inputs["spim"].wildcards,
),
seg=atlas_segs,
desc=config["seg_method"],
template=config["template"],
suffix=config["coloc_seg_metrics"],
),
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
stain="{stain}",
desc="{desc}",
space="{template}",
suffix="regqc.html",
suffix="coloccounts.nii.gz",
**inputs["spim"].wildcards,
),
stain=stain_for_reg,
desc=config["seg_method"],
template=config["template"],
),

Expand Down Expand Up @@ -375,14 +381,6 @@ rule all_imaris_crops:
),


rule all:
default_target: True
input:
rules.all_segment.input,
rules.all_spim_patches.input,
rules.all_mri_reg.input if config["register_to_mri"] else [],


rule all_group_stats:
"""Target rule for group-level statistical analysis."""
input:
Expand Down Expand Up @@ -421,62 +419,73 @@ rule all_group_stats:
bids(
root=root,
datatype="group",
seg="{seg}",
level="{level}",
space="{template}",
desc="{desc}",
metric="coloc+{metric}",
suffix="{stat}.nii.gz",
suffix="{stain}+count.nii.gz",
),
seg=atlas_segs,
desc=config["seg_method"],
template=config["template"],
metric=config["coloc_seg_metrics"],
stat=config["stats_maps"],
level=range(4),
stain=stains_for_seg,
),
# Add contrast-filtered outputs
expand(
bids(
root=root,
datatype="group",
level="{level}",
space="{template}",
desc="{desc}",
suffix="{stain}+count.nii",
contrast="{contrast_column}+{contrast_value}",
suffix="{stain}+count.nii.gz",
),
desc=config["seg_method"],
template=config["template"],
level=range(4),
stain=stains_for_seg,
contrast_column=config["contrast_column"],
contrast_value=config["contrast_values"],
),
# Add group-averaged segstats maps by contrast
expand(
bids(
root=root,
datatype="group",
seg="{seg}",
space="{template}",
level="{level}",
desc="{desc}",
suffix="coloccount.nii",
contrast="{contrast_column}+{contrast_value}",
metric="{stain}+{metric}",
suffix="groupavg.nii.gz",
),
seg=atlas_segs,
desc=config["seg_method"],
template=config["template"],
level=range(4),
stain=stains_for_seg,
metric=config["seg_metrics"],
contrast_column=config["contrast_column"],
contrast_value=config["contrast_values"],
),
# Add contrast-filtered outputs


rule all_group_stats_coloc:
input:
expand(
bids(
root=root,
datatype="group",
level="{level}",
seg="{seg}",
space="{template}",
desc="{desc}",
contrast="{contrast_column}+{contrast_value}",
suffix="{stain}+count.nii",
metric="coloc+{metric}",
suffix="{stat}.nii.gz",
),
seg=atlas_segs,
desc=config["seg_method"],
template=config["template"],
level=range(4),
stain=stains_for_seg,
contrast_column=config["contrast_column"],
contrast_value=config["contrast_values"],
metric=config["coloc_seg_metrics"],
stat=config["stats_maps"],
),
expand(
bids(
Expand All @@ -485,32 +494,25 @@ rule all_group_stats:
space="{template}",
level="{level}",
desc="{desc}",
contrast="{contrast_column}+{contrast_value}",
suffix="coloccount.nii",
suffix="coloccount.nii.gz",
),
desc=config["seg_method"],
template=config["template"],
level=range(4),
contrast_column=config["contrast_column"],
contrast_value=config["contrast_values"],
),
# Add group-averaged segstats maps by contrast
expand(
bids(
root=root,
datatype="group",
seg="{seg}",
space="{template}",
level="{level}",
desc="{desc}",
contrast="{contrast_column}+{contrast_value}",
metric="{stain}+{metric}",
suffix="groupavg.nii.gz",
suffix="coloccount.nii.gz",
),
seg=atlas_segs,
desc=config["seg_method"],
template=config["template"],
stain=stains_for_seg,
metric=config["seg_metrics"],
level=range(4),
contrast_column=config["contrast_column"],
contrast_value=config["contrast_values"],
),
Expand All @@ -534,7 +536,21 @@ rule all_group_stats:
),


include: "rules/common.smk"
rule all_participant:
default_target: True
input:
rules.all_segment.input,
rules.all_spim_patches.input,
rules.all_mri_reg.input if config["register_to_mri"] else [],
rules.all_segment_coloc.input if do_coloc else [],


rule all_group:
input:
rules.all_group_stats.input,
rules.all_group_stats_coloc.input if do_coloc else [],


include: "rules/import.smk"
include: "rules/masking.smk"
include: "rules/templatereg.smk"
Expand Down
12 changes: 12 additions & 0 deletions spimquant/workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -34,3 +34,15 @@ def get_template_for_reg(wildcards):
return get_template_path(root, wildcards.template, config["template_crop"])
else:
return bids_tpl(root=root, template=wildcards.template, suffix="anat.nii.gz")


def get_stains_all_subjects():

stain_sets = [
set(ZarrNii.from_ome_zarr(zarr).list_channels())
for zarr in inputs["spim"].expand()
]
if all(s == stain_sets[0] for s in stain_sets):
return list(stain_sets[0])
else:
raise ValueError(f"stains across subjects are not consistent, {stain_sets}")
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