wbwakeman

--95 human, 527 mouse= 622 reconstructions for June 2020
SELECT p.code AS csp_project, d.organism_id, csp.id AS csp_id, csp.name AS csp, csp.patched_cell_container, csp.ephys_qc_result AS csp_eqr, err.id AS err_id, err.workflow_state AS err_state, 
nrwkf.storage_directory || nrwkf.filename AS nrwkf, a.name AS age, d.external_donor_name
,st.acronym AS csp_structure, cr.name AS cell_reporter_name, csl.id AS csl_id, csl.normalized_depth, err.published_at AS err_published, nrwkf.published_at AS nrwkf_published
,sta.name AS apical_specimen_tag, std.name AS dendrite_specimen_tag
FROM specimens csp JOIN specimens sp ON sp.id=csp.parent_id JOIN donors d ON sp.donor_id=d.id JOIN projects p ON p.id=csp.project_id LEFT JOIN ephys_roi_results err ON csp.ephys_roi_result_id=err.id 
JOIN ages a ON a.id=d.age_id 
JOIN structures st ON st.id=csp.structure_id 
JOIN cell_reporters cr ON cr.id=csp.cell_reporter_id
JOIN cell_soma_locations csl ON csl.specimen_id=csp.id

wbwakeman

{
   "specimen_id":1234,
   "kind":"IVSCC cell locations",
   "data":{
      "DefaultCameraPosition":[
         5873.05421548901,
         -54260.69374827002,
         -4027.878783549626
      ],
      "DefaultCameraViewUp":[

wbwakeman

{
    "DefaultCameraPosition": [
        5843.63200143959,
        -51647.244976327915,
        -4001.1474083390378
    ],
    "DefaultCameraViewUp": [
        0.0,
        0.0,
        1.0

wbwakeman

import sys
import os
import h5py
import scipy.ndimage.measurements as measurements
import numpy as np
#import Queue
import math
from PIL import Image
from pylab import *

wbwakeman

{
   "upload_order":[
      "probe_info",
      "unit_metrics",
      "manual_channel_structures"
   ],
   "expected_files":{
      "lfp_data":{
         "subtype":"EcephysSortedLfpContinuous",
         "required":true,

wbwakeman

[
   {
      "id":1065522445,
      "name":"AIBS0001_488.00",
      "created_at":"2020-11-23T20:11:10.663-08:00",
      "updated_at":"2020-11-23T20:11:10.663-08:00",
      "concentrate_name":"AIBS0001_488",
      "zhuang_readout":"RS0015",
      "sanctioned_for_barcode_panels":true,
      "archived":false,

wbwakeman

FAILURE - NWAY CELL MATCHING (21)
782536745
812858755
814796558
1018027781
1018027884
1018027896
1026722854
1026722861
1026722864

wbwakeman

import matplotlib.figure as mplt_figure
from numpy.core.fromnumeric import size
import pandas as pd
import imageio

#######################################################
#      sst = 3
fig = mplt_figure.Figure(figsize=(60,45))
axes = [fig.add_subplot(6, 6, ii) for ii in range(1,37,1)]
# fig.suptitle('Multiple experiments, smooth_sigma_time = 5', size=35)

wbwakeman

import matplotlib.figure as mplt_figure
from numpy.core.fromnumeric import size
import pandas as pd
import imageio

#######################################################
#      sst = 5
fig = mplt_figure.Figure(figsize=(60,10))
axes = [fig.add_subplot(1, 6, ii) for ii in range(1,7,1)]
# fig.suptitle('Multiple experiments, smooth_sigma_time = 5', size=35)

wbwakeman

{
   "markups":[
      {
         "name":"Gad2-IRES-Cre;Ai14-600202.11.02.01",
         "structure_id": 362,
         "structure_acronym":"MD"
         "markup":{
            "type":"Fiducial",
            "controlPoints":[
               {