This is a neuro 'informatics' tutorial we ran at the 2015 graduate research orientation.

See more info at brain-map website and AllenBrainAtlas on github.

1. Test Allen Brain Institute mouse connectivity web interface

http://connectivity.brain-map.org/

Search for Secondary Visual source injections sites:

  • Look for several injections across VISl or VISal
    • Make note of the experiment id no. for each here:
      • id1 = 263780729
      • id2 =100141796
      • id3 =167794131
      • id4 =
      • ...

2. Render and explore datasets in 3D

Open each of the selected datasets in Brain Explorer (click the 3D button from the web interface).

  • Render the injections in different colors in Brain Explorer desktop software
  • Create snapshots (shift-cmd-4), drag onto the mv2imgFolder.app function on the Desktop, and paste into this markdown text file:

3. Use allensdk to download and plot multiple experiments

First open the command line terminal (cmd-spacebar, search for terminal).

Type in the following:

cd ~/Desktop
mkdir 20150915_visual_connect
cd 20150915_visual_connect
ipython --pylab

Download selected experiment data

#enter selected projection numbers here, e.g. 167794131, 297231636, 287495026
id1 = 167794131
id2 = 297231636
id3 = 272736450

# import allensdk python api
from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi
mca = MouseConnectivityApi()

# get metadata for all experiments
experiments = mca.experiment_source_search(injection_structures=['VIS','PTLp','RSP'])

# find selected experiments and format filenames, **Use the %paste magic function if pasting into ipython
for i in range(len(experiments)):
    if (experiments[i]['id'] == id1):
        fn1 = str(experiments[i]['injection-structures'][0]['abbreviation']) + '_' + str(experiments[i]['id']) + '_' + str(experiments[i]['transgenic-line'])
    if (experiments[i]['id'] == id2):
        fn2 = str(experiments[i]['injection-structures'][0]['abbreviation']) + '_' + str(experiments[i]['id']) + '_' + str(experiments[i]['transgenic-line'])
    if (experiments[i]['id'] == id3):
        fn3 = str(experiments[i]['injection-structures'][0]['abbreviation']) + '_' + str(experiments[i]['id']) + '_' + str(experiments[i]['transgenic-line'])

# download selected experiment projection density files at 25 µm resolution
mca.download_projection_density(fn1 + '.nrrd', id1, resolution=25)
mca.download_projection_density(fn2 + '.nrrd', id2, resolution=25)
mca.download_projection_density(fn3 + '.nrrd', id3, resolution=25)

Plot projection density images

import datetime, nrrd

A1, metadata1 = nrrd.read(fn1 + '.nrrd')
A1.shape

imshow(A1[300,:,:])

mxProj1 = amax(A1,0)  #second input is the dimension you want to project over
imshow(mxProj1)

Make multicolor projection images

filenames = [fn1, fn2, fn3]
A1, metadata1 = nrrd.read(filenames[0] + '.nrrd')
A2, metadata2 = nrrd.read(filenames[1] + '.nrrd')
A3, metadata2 = nrrd.read(filenames[2] + '.nrrd')

def rgbMaxProj(A1,A2,A3,dim):
  mxProj1 = amax(A1,dim)
  mxProj2 = amax(A2,dim)
  mxProj3 = amax(A3,dim)
  rgbA = zeros((mxProj1.shape[0],mxProj1.shape[1],3))
  rgbA[...,0] += mxProj1
  rgbA[...,1] += mxProj2
  rgbA[...,2] += mxProj3
  return rgbA

figure(dpi=300)
subplot(131)
rgbA = rgbMaxProj(A1,A2,A3,0)
ax1=imshow(rgbA,interpolation=None)

subplot(132)
rgbA = rgbMaxProj(A1,A2,A3,1)
ax2=imshow(rgbA,interpolation=None)

subplot(133)
rgbA = rgbMaxProj(A1,A2,A3,2)
ax3=imshow(rgbA,interpolation=None)
title('r:' + filenames[0] + ', g:' + filenames[1] + ', b:' + filenames[2])

dateStr = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
rcParams['pdf.fonttype'] = 42
savefig(dateStr + '.png')
savefig(dateStr + '.pdf',dpi=300)

Download and automatically save multiple plots for a bunch of experiments

Look at VISam, PTLp, RSP projections

from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi

mca = MouseConnectivityApi()

# get metadata for all experiments
experiments = mca.experiment_source_search(injection_structures=['PTLp','VISam','RSP'])

# download the projection density volume for one of the experiments. This will also download and save the file in the local folder as well as storing it as a variable.
#pd = mca.download_projection_density('example.nrrd', experiments[0]['id'], resolution=25)
for i in range(len(experiments)):
  filename = str(experiments[i]['injection-structures'][0]['abbreviation']) + '_' + str(experiments[i]['id']) + '_' + str(experiments[i]['transgenic-line'])
  print filename
  mca.download_projection_density(filename + '.nrrd', experiments[i]['id'], resolution=25)

Save the printed filenames as a text file 2015-09-15_experiments.txt with one filename per line.

fn = "2015-09-15_experiments.txt"
with open(fn) as f:
    data = f.read().splitlines()

def print3chan(fn1,fn2,fn3):
  A1, metadata1 = nrrd.read(fn1 + '.nrrd')
  A2, metadata2 = nrrd.read(fn2 + '.nrrd')
  A3, metadata2 = nrrd.read(fn3 + '.nrrd')
  #plot images as multiplot
  fig=figure(1,dpi=300)
  subplot(131)
  rgbA = rgbMaxProj(A1,A2,A3,0)
  ax1=imshow(rgbA,interpolation=None)
  subplot(132)
  rgbA = rgbMaxProj(A1,A2,A3,1)
  ax2=imshow(rgbA,interpolation=None)
  title('r:' + fn1 + '\n g:' + fn2 + '\n b:' + fn3)
  subplot(133)
  rgbA = rgbMaxProj(A1,A2,A3,2)
  ax3=imshow(rgbA,interpolation=None)
  #save fig
  dateStr = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
  rcParams['pdf.fonttype'] = 42
  savefig(dateStr + '.png')
  savefig(dateStr + '.pdf',dpi=300)
  close(fig)

def rgbMaxProj(A1,A2,A3,dim):
  mxProj1 = amax(A1,dim)
  mxProj2 = amax(A2,dim)
  mxProj3 = amax(A3,dim)
  rgbA = zeros((mxProj1.shape[0],mxProj1.shape[1],3))
  rgbA[...,0] += mxProj1
  rgbA[...,1] += mxProj2
  rgbA[...,2] += mxProj3
  return rgbA

for i in arange(len(data),step=3):
  j = i + 1
  k = i + 2
  if (abs(i - arange(len(data))[-1]) < 2):
    k = 0
    if (abs(i - arange(len(data))[-1]) < 1):
      j = 0
      k = 1
  print3chan(data[i],data[j],data[k])