Това проработи:
pipeline = [{'$lookup':
{'from' : 'models',
'localField' : '_id',
'foreignField' : 'references',
'as' : 'cellmodels'}},
{'$unwind': '$cellmodels'},
{'$match':
{'authors' : 'Migliore M', 'cellmodels.celltypes' : 'Hippocampus CA3 pyramidal cell'}},
{'$project':
{'authors':1, 'cellmodels.celltypes':1}}
]
for doc in (papers.aggregate(pipeline)):
pprint (doc)