Valentina Staneva valentina-s

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Background

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On Instance:

pip install jupyter[notebook]

jupyter notebook --generate-config

# nano .jupyter/jupyter_notebook_config.py

echo "c = get_config()
c.NotebookApp.ip = '*'

Setup Python Environment

Instructions to run the tutorial notebooks for the [Allen Brain Observatory dataset] (http://observatory.brain-map.org/visualcoding/sdk/index).

Install Python from https://www.continuum.io/downloads.

Install git https://git-scm.com/book/en/v2/Getting-Started-Installing-Git

(On Windows use git bash as a shell to run the following commands)

	import math
	def calculate_xy(lat,lon,z):
	latRad = lat * math.pi / 180;
	n = math.pow(2, z);
	xTile = n * ((lon + 180) / 360);
	yTile = n * (1-(math.log(math.tan(latRad) + 1/math.cos(latRad))/math.pi)) / 2;
	return(xTile,yTile)

	def get_api_keys(keys_file):
	keys = []

	#!/usr/bin/env python

	import vtk
	import sys

	filename = sys.argv[1]

	reader = vtk.vtkSTLReader()
	reader.SetFileName(filename)

	import numpy as np
	import matplotlib.pyplot as plt
	im = plt.imread('cells.png')
	fig = plt.figure()
	ax = fig.add_subplot(111)
	# ax.add_image(im)
	plt.imshow(im)
	coords = []
	import cell_magic_wand

	<!DOCTYPE html>
	<html>
	<head><meta charset="utf-8" />
	<title>NumberOfTopicsSelection</title>

	<script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script>

	<style type="text/css">
	/*!