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Add ndtypes from ndx-pose, ndx-photometry, ndx-fiber-photometry #1665

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3e86325
Add ndtypes from ndx-pose, ndx-photometry, ndx-fiber-photometry
rly Jul 23, 2025
da8c29b
Merge branch 'master' into add_ndtypes
CodyCBakerPhD Aug 14, 2025
3d7baea
Update dandi/metadata/util.py
CodyCBakerPhD Aug 26, 2025
00a60ad
Merge branch 'master' into add_ndtypes
CodyCBakerPhD Aug 26, 2025
1b99658
Update dandi/metadata/util.py
rly Aug 27, 2025
d360e2d
Update dandi/metadata/util.py
rly Aug 27, 2025
5e48759
Update dandi/metadata/util.py
rly Aug 27, 2025
21b1d99
Update dandi/metadata/util.py
rly Aug 27, 2025
20394ff
Update metadata for various neurodata types
rly Aug 27, 2025
6ad64c1
Update test_metadata.py
rly Aug 27, 2025
0648a40
Fix whitespace lint error
rly Aug 27, 2025
7dddd60
Update technique description for PoseTraining
rly Aug 27, 2025
7fcddb8
Update test_metadata.py
rly Aug 27, 2025
c268842
Update test_metadata.py
rly Aug 28, 2025
9571b6b
Merge branch 'master' into add_ndtypes
rly Aug 28, 2025
bfc4553
Merge branch 'master' into add_ndtypes
yarikoptic Sep 16, 2025
60c21ab
Merge branch 'master' into add_ndtypes
rly Sep 17, 2025
f8490a9
Change Units module from 'misc' to 'sortedunits'
rly Sep 17, 2025
4269177
Add draft more complete neurodata type map
rly Sep 17, 2025
c25e3d2
Apply my first edits to neurodata_typemap.py
rly Sep 17, 2025
a6d1cb2
Apply edits from review
rly Sep 17, 2025
b784ba3
Sort neurodata_typemap.py
rly Sep 17, 2025
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34 changes: 32 additions & 2 deletions dandi/metadata/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -828,9 +828,9 @@ class Neurodatum(TypedDict):
"technique": "fourier analysis technique",
"approach": None,
},
"OptogeneticStimulusSIte": {
"OptogeneticStimulusSite": {
"module": "ogen",
"neurodata_type": "OptogeneticStimulusSIte",
"neurodata_type": "OptogeneticStimulusSite",
"technique": None,
"approach": "optogenetic approach",
},
Expand All @@ -840,6 +840,36 @@ class Neurodatum(TypedDict):
"technique": None,
"approach": "optogenetic approach",
},
"PoseEstimationSeries": {
"module": "ndx-pose",
"neurodata_type": "PoseEstimationSeries",
"technique": "pose estimation technique",
"approach": "behavioral approach",
},
"PoseEstimation": {
"module": "ndx-pose",
"neurodata_type": "PoseEstimation",
"technique": "pose estimation technique",
"approach": "behavioral approach",
},
"PoseTraining": {
"module": "ndx-pose",
"neurodata_type": "PoseTraining",
"technique": "pose estimation technique",
"approach": "behavioral approach",
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@satra satra Aug 26, 2025

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on a more general note, i'm a bit confused about why pose training is a data type, as that doesn't seem to reflect behavior per se, and also why it is a pose estimation technique.

some of these are direct measurement techniques or estimation techniques, but this one seems odd.

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@rly rly Aug 27, 2025

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PoseTraining is a group consisting of training frames and source videos. A training frame refers to a frame from a source video and an the locations of each node of 1 or more skeletons, often from human labeling. So PoseTraining isn't exactly a data type but indicative of the NWB file containing training data for pose estimation methods. Should I pick out a different data type to detect instead?

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@satra satra Aug 27, 2025

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we should consider data type as a broad umbrella of what data is generated from or used for (for example there is fourier analysis above). it could be associated with a "pose estimation training technique"

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@rly rly Aug 27, 2025

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got it. that makes sense

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@yarikoptic yarikoptic Sep 22, 2025

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@rly here we have 2 extensions listed to assist with importing https://github.com/dandi/dandi-cli/blob/HEAD/dandi/metadata/nwb.py#L99 -- should we also add extension information into this 'registry' and use it there too? or may be it is no longer even needed?

},
"FiberPhotometryResponseSeries": {
"module": "ndx-fiber-photometry",
"neurodata_type": "FiberPhotometryResponseSeries",
"technique": "fiber photometry technique; optical technique",
"approach": "calcium imaging; cell population imaging",
},
"FiberPhotometryResponseSeries_old": {
"module": "ndx-photometry", # deprecated and replaced by ndx-fiber-photometry
"neurodata_type": "FiberPhotometryResponseSeries",
"technique": "fiber photometry technique; optical technique",
"approach": "calcium imaging; cell population imaging",
},
}


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44 changes: 42 additions & 2 deletions dandi/tests/test_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -788,11 +788,11 @@ def test_species_map():
},
),
(
["OptogeneticStimulusSIte"],
["OptogeneticStimulusSite"],
{
"approach": ["optogenetic approach"],
"measurementTechnique": None,
"variableMeasured": ["OptogeneticStimulusSIte"],
"variableMeasured": ["OptogeneticStimulusSite"],
},
),
(
Expand All @@ -803,6 +803,46 @@ def test_species_map():
"variableMeasured": ["OptogeneticSeries"],
},
),
(
["PoseEstimationSeries"],
{
"approach": ["behavioral approach"],
"measurementTechnique": ["pose estimation technique"],
"variableMeasured": ["PoseEstimationSeries"],
},
),
(
["PoseEstimation"],
{
"approach": ["behavioral approach"],
"measurementTechnique": ["pose estimation technique"],
"variableMeasured": ["PoseEstimation"],
},
),
(
["PoseTraining"],
{
"approach": ["behavioral approach"],
"measurementTechnique": ["pose estimation technique"],
"variableMeasured": ["PoseTraining"],
},
),
(
["FiberPhotometryResponseSeries"],
{
"approach": ["fiber photometry technique; optical technique"],
"measurementTechnique": ["calcium imaging; cell population imaging"],
"variableMeasured": ["FiberPhotometryResponseSeries"],
},
),
(
["FiberPhotometryResponseSeries_old"],
{
"approach": ["fiber photometry technique; optical technique"],
"measurementTechnique": ["calcium imaging; cell population imaging"],
"variableMeasured": ["FiberPhotometryResponseSeries"],
},
),
(
# the tricky case of having number of instances of the data type
# https://github.com/dandi/dandi-cli/issues/890
Expand Down
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