reconstrue / brightfield

Reconstruction of biocytin-stained neurons detected in brightfield microscopy image stacks
http://reconstrue.com
Apache License 2.0
2 stars 1 forks source link

Mimic allensdk's Cell Types API #60

Open JohnTigue opened 5 years ago

JohnTigue commented 5 years ago

The Challenge data will eventually be in brain-map.org. So, mimic that API for fetching.

Not sure how to get image stack out of allensdk. Yeah, out of RMA RESTful but not the SDK. So, this may be a Reconstrue thing: one way to ask for image stack and swc that spans both Wasabi and brain-map.org

From the Cell Types docs:

ctc = CellTypesCache(manifest_file='cell_types/manifest.json')

# a list of cell metadata for cells with reconstructions, download if necessary
cells = ctc.get_cells(require_reconstruction=True)

# open the electrophysiology data of one cell, download if necessary
data_set = ctc.get_ephys_data(cells[0]['id'])

# read the reconstruction, download if necessary
reconstruction = ctc.get_reconstruction(cells[0]['id'])

So, then the PR would add:

image_stack = ctc.get_image_stack(some_cell_id)

Then, can run the visualizers on Allen's raw data.

Also, see #50.

JohnTigue commented 5 years ago

Dr. Collman says this is indeed a feature that is not yet part of allensdk as it is not a feature that has been requested frequently.