In [1]:

import pymaid

# We will deactivate caching so that we always have the live data
rm = pymaid.connect_catmaid(caching=False)

INFO  : Global CATMAID instance set. Caching is OFF. (pymaid)

In [3]:

resp = pymaid.add_annotations(16, "favourite neuron of Philipp")

In [4]:

resp

Out[4]:

{'message': 'success',
 'annotations': [{'name': 'favourite neuron of Philipp',
   'id': 16954141,
   'entities': [17]}],
 'new_annotations': [16954141],
 'existing_annotations': []}

In [5]:

pymaid.get_skids_by_annotation('favourite neuron of Philipp')

Out[5]:

[16]

In [6]:

resp = pymaid.remove_annotations(16, 'favourite neuron of Philipp')
resp

INFO  : Removed "favourite neuron of Philipp" from 1 entities (0 uses left) (pymaid)

Out[6]:

{'deleted_annotations': {'16954141': {'targetIds': [17]}},
 'deleted_links': [16954142],
 'left_uses': {'16954141': 0}}

In [7]:

import navis
import pandas as pd

# Create node table
node_table = pd.DataFrame([[0, -1,  0,  0,  0, -1],
                           [1,  0, 10, 10, 10, -1]],
                          columns=['node_id', 'parent_id', 'x', 'y', 'z', 'radius'])
# Turn node table into navis neuron
n = navis.TreeNeuron(node_table)
n

Out[7]:


type	navis.TreeNeuron
name	None
n_nodes	2
n_connectors	None
n_branches	0
n_leafs	None
cable_length	17.3205
soma	None
units	1 dimensionless

In [8]:

# Upload neuron to our CATMAID server
resp = pymaid.upload_neuron(n)
resp

Out[8]:

{'neuron_id': 16954144,
 'skeleton_id': 16954143,
 'node_id_map': {0: 66611224, 1: 66611225}}

In [3]:

pymaid.get_neuron(resp['skeleton_id'])

HBox(children=(HTML(value='Make nrn'), FloatProgress(value=0.0, max=1.0), HTML(value='')))

Out[3]:


type	CatmaidNeuron
name	neuron 16954144
id	16954143
n_nodes	2
n_connectors	0
n_branches	0
n_leafs	None
cable_length	17.3205
soma	None
units	1 nanometer

In [5]:

_ = pymaid.rename_neurons(resp['skeleton_id'], 'Philipps mock neuron')
pymaid.get_names(resp['skeleton_id'])

      Current name              New name Skeleton ID
0  neuron 16954144  Philipps mock neuron    16954143
Please confirm above renaming [Y/N] y

INFO  : All neurons successfully renamed. (pymaid)

Out[5]:

{'16954143': 'Philipps mock neuron'}

In [6]:

pymaid.delete_neuron(resp['skeleton_id'])

Neuron "Philipps mock neuron" (#16954143) has 2 nodes (0 reviewed) and 1 annotation(s)
Please confirm deletion [Y/N] y

Out[6]:

{'skeleton_ids': [16954143],
 'success': 'Deleted neuron #16954144 as well as its skeletons and annotations.'}