Trouble Fetching Generalized Group of Neurons + General Question

[Jordan Imani Kalai]

Hello,

I am having trouble selecting a group of neurons using '.*' to select a group. For example,  when I run 

neurons_df, roi_counts_df = fetch_neurons(NC(type='MBON.*'))

an empty data frame is returned, but if I specify the name of each neuron such as 

cells = ['FB6A', 'FB6C_a', 'FB6C_b', 'FB6E', 'FB6G', 'FB6I', 'FB6Z', 'FB7A', 'FB7K']

criteria = NC(type=cell)
neurons_df, roi_counts_df = neuprint.fetch_neurons(criteria)

then a non-empty data frame is returned as expected. I have tried following the example as explained here, but have struggled to get any category of neurons specified with .* to lead to anything besides an empty data frame. Any help would be appreciated.

Additionally, if I was looking to meet virtually with someone who would be able to explain some of the neuprint tools/ Navis cross-functionality,  who would be a good person to contact? I am looking to segment neuronal cross-sectional area and mitochondrial cross-sectional area for a given neuron and while I understand components the process, I would love to meet with someone to have a more in-depth conversation if possible.

[Berg, Stuart]

Hi Jordan,

I am having trouble selecting a group of neurons using '.*' to select a group. For example,  when I run 

neurons_df, roi_counts_df = fetch_neurons(NC(type='MBON.*'))

an empty data frame is returned

What version of neuprint-python are you using? Older versions of neuprint-python required you to specify whether or not your supplied 'type' should be interpreted as an exact string or a regular expression (via regex=True).  Newer versions will automatically guess your intent (unless you override that guess).

https://connectome-neuprint.github.io/neuprint-python/docs/changelog.html

The following works for me.  All three of these lines are equivalent, and return 71 results.

neurons, roicounts = fetch_neurons('MBON.*')

neurons, roicounts = fetch_neurons(NC(type='MBON.*'))

neurons, roicounts = fetch_neurons(NC(type='MBON.*', regex=True))

I don't have expertise in Navis, but I can ask around.

Best,

Stuart

[Philipp Schlegel]

Hi Jordan. I might be able to help you with navis. If you send me a private message with your email we can try arranging a meeting.

Best,

Philipp