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Wayne Wakeman wbwakeman

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@wbwakeman
wbwakeman / 202203110909_pbs1874_datafix.rb
Created March 11, 2022 19:36
This is an update of Nile's 2019 datafix script that uploads Neuropixels ccf infomation from ccf_regions.csv files to the LIMS2 ecephys_channels table
class Pbs1874Datafix < AIBS::Datafix
# https://github.com/AllenInstitute/AllenSDK/issues/992
# http://stash.corp.alleninstitute.org/projects/TECH/repos/lims/browse/db/datafixes/20190911134728_pbs1874_datafix.rb?at=ac873b70756defe209124330f8723f1e99de03c3
#create_ldds_row # this mandatory statement belongs at the beginning of the script since part of the purpose of this class is to determine if your datafix script has already been run. (see http://confluence.corp.alleninstitute.org/display/IT/datafix).
structures = {}
acro_id = {}
isocortical = []
layer = Set.new
@wbwakeman
wbwakeman / 20220218_example.json
Created February 18, 2022 20:29
{
"markups":[
{
"name":"Gad2-IRES-Cre;Ai14-600202.11.02.01",
"structure_id": 362,
"structure_acronym":"MD"
"markup":{
"type":"Fiducial",
"controlPoints":[
{
@wbwakeman
wbwakeman / mesoscope_motion_correction_final_ploy.py
Created September 3, 2021 21:48
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
wbwakeman / mesoscope_motion_correction_manual_ploy.py
Created September 3, 2021 21:47
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
wbwakeman / visual behavior container ids 20201124
Created November 24, 2020 15:46
FAILURE - NWAY CELL MATCHING (21)
782536745
812858755
814796558
1018027781
1018027884
1018027896
1026722854
1026722861
1026722864
@wbwakeman
wbwakeman / 20201123_readout_oligos
Created November 24, 2020 04:16
[
{
"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
wbwakeman / gist:a3f81e9ce76738262341cd892082076e
Last active October 12, 2020 19:14
20201012_ecephys_session_upload_queue_static_data
{
"upload_order":[
"probe_info",
"unit_metrics",
"manual_channel_structures"
],
"expected_files":{
"lfp_data":{
"subtype":"EcephysSortedLfpContinuous",
"required":true,
@wbwakeman
wbwakeman / gist:b8719e0ad5b1b6486482974f410ab086
Last active January 13, 2022 17:45
sine_dewarp_grid
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
wbwakeman / 20170213_297662.003.15.json
Created September 25, 2020 23:04
Cell Locator json file from May 2020
{
"DefaultCameraPosition": [
5843.63200143959,
-51647.244976327915,
-4001.1474083390378
],
"DefaultCameraViewUp": [
0.0,
0.0,
1.0
@wbwakeman
wbwakeman / annotation_stub_to_POST.json
Last active July 14, 2020 00:01
{
"specimen_id":1234,
"kind":"IVSCC cell locations",
"data":{
"DefaultCameraPosition":[
5873.05421548901,
-54260.69374827002,
-4027.878783549626
],
"DefaultCameraViewUp":[