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Add subjects metadata #20

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merged 1 commit into from
May 23, 2024
Merged

Add subjects metadata #20

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8 changes: 8 additions & 0 deletions src/dombeck_lab_to_nwb/azcorra2023/azcorra2023_convert_session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,14 @@ def session_to_nwb(
editable_metadata = load_dict_from_file(editable_metadata_path)
metadata = dict_deep_update(metadata, editable_metadata)

subjects_metadata_path = Path(__file__).parent / "metadata" / "azcorra2023_subjects_metadata.yaml"
subjects_metadata = load_dict_from_file(subjects_metadata_path)
subject_type = processed_photometry_mat_file_path.stem.split("-")[0]
subject_metadata = subjects_metadata["Subjects"][subject_type]
virus_metadata = subject_metadata.pop("virus")
metadata["Subject"].update(subject_metadata)
metadata["NWBFile"].update(virus=virus_metadata)

fiber_photometry_metadata = load_dict_from_file(
Path(__file__).parent / "metadata" / "azcorra2023_fiber_photometry_metadata.yaml"
)
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4 changes: 0 additions & 4 deletions src/dombeck_lab_to_nwb/azcorra2023/azcorra2023_metadata.yaml
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Expand Up @@ -24,7 +24,6 @@ NWBFile:
lab: Dombeck
experimenter:
- Azcorra, Maite
virus: AAV8-EF1α-CreOn/FlpOn-GCaMP6f (RRID:Addgene_137122, titer 6.10 × 1013)
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Removed as it depends on which subject type is added.

pharmacology: |
Adult mice (postnatal 2–4 months old) were anesthetized with isoflurane (1–2%), and a 0.5–1-mm-diameter craniotomy
was made over the right substantia nigra (−3.25 mm caudal, +1.55 mm lateral from bregma).
Expand All @@ -38,6 +37,3 @@ NWBFile:
endogenously, no injection was conducted, and only the headplate was implanted at this time. Four weeks were
allowed for GCaMP6f expression to ramp up and fill dopaminergic somas in SNc and axons in striatum.
protocol: https://doi.org/10.17504/protocols.io.5qpvor8zxv4o/v1
Subject:
species: Mus musculus
age: P8W/P16W
34 changes: 34 additions & 0 deletions src/dombeck_lab_to_nwb/azcorra2023/metadata/azcorra2023_subjects_metadata.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
Subjects:
Anxa:
genotype: Anxa1-iCre
strain: C57BL6
description: The Anxa1-iCre lines were generated at Northwestern University by the Transgenic and Targeted Mutagenesis Laboratory.
virus: AAV1-CAG-FLEX-GCaMP6f virus injected in SNc (RRID, Addgene_100835)
species: Mus musculus
age: P8W/P16W
Calb:
genotype: Calb1-IRES2-Cre/DAT-tTA/Ai93D # Calb1-IRES2-Cre/Th-Flpo
strain: C57BL6
virus: AAV1-CAG-FLEX-GCaMP6f virus injected in SNc (RRID, Addgene_100835)
species: Mus musculus
age: P8W/P16W
Dat:
genotype: DAT-IRES-Cre (RRID, IMSR_JAX:027178)
strain: C57BL6
virus: AAV1-CAG-FLEX-GCaMP6f virus injected in SNc (RRID, Addgene_100835)
species: Mus musculus
age: P8W/P16W
# GrabDA:
Raldh:
genotype: Aldh1a1-iCre/Th-Flpo
strain: C57BL6
description: The Aldh1a1-iCre lines were generated at Northwestern University by the Transgenic and Targeted Mutagenesis Laboratory.
virus: AAV8-EF1α-CreOn/FlpOn-GCaMP6f virus (RRID, Addgene_137122)
species: Mus musculus
age: P8W/P16W
VGlut:
genotype: Vglut2-IRES-Cre/Th-Flpo (RRID, IMSR_JAX:016963)
strain: C57BL6
virus: AAV8-EF1α-CreOn/FlpOn-GCaMP6f virus (RRID, Addgene_137122)
species: Mus musculus
age: P8W/P16W
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