Download all images from an imageseries from Allen Developing Mouse Brain Atlas - python 3

imageseries_download.py

import urllib.request, json
import os

#
# Example python code to download images from an image series
#
# Find the image series you want from the Allen Brain Atlas portal
# Take a note of the dataset id
#

# Specify output directory for images
output_directory = "temp/dataset"

# Specify downsample factor; recommend using 1 for developing mouse brain images @ younger ages
downsample = 1

# Copy the dataset id here
dataset_id = 100045958

# make output directory
if not os.path.exists( output_directory ) :
    os.makedirs( output_directory )

# RMA query to get information for images in the dataset
query_url  = "http://api.brain-map.org/api/v2/data/query.json?"
query_url += "criteria=model::SectionImage"
query_url += ",rma::criteria,[data_set_id$eq%d]" % (dataset_id)
query_url += ",rma::options[num_rows$eqall]" 

response = urllib.request.urlopen (query_url)
images = json.loads(response.read())['msg']
    
for i in images :
    print (i['section_number'], i['id'])
    image_url  = "http://api.brain-map.org/api/v2/section_image_download/%d?downsample=%d" % (i['id'],downsample)
    image_path = os.path.join( output_directory, '%04d_%d.jpg' % (i['section_number'],i['id'])    )
    urllib.request.urlretrieve(image_url, image_path)