Added download_data_local.py and updated 5.1 Filtering

course_functions.py

@@ -23,12 +23,12 @@ def detect_nuclei(image, size = 200):
     """
 
     # filtering
-    image = skimage.filters.median(image,selem=np.ones((2,2)))
+    image = skimage.filters.median(image,footprint=np.ones((2,2)))
     # local thresholding
     image_local_threshold = skimage.filters.threshold_local(image,block_size=51)
     image_local = image > image_local_threshold
     # remove tiny features
-    image_local_open = skimage.morphology.binary_opening(image_local, selem=skimage.morphology.disk(2))
+    image_local_open = skimage.morphology.binary_opening(image_local, footprint=skimage.morphology.disk(2))
     # label image
     image_labeled = label(image_local_open)
     # analyze regions

installation/download_data_local.py

@@ -0,0 +1,89 @@
+import sys, os, zipfile, tarfile
+import urllib.request
+import requests
+
+# Direct download from Zenodo
+if not os.path.exists('../Data/'):
+    os.makedirs('../Data/')
+    url = 'https://zenodo.org/record/3856637/files/Data.zip?download=1'
+    urllib.request.urlretrieve(url, '../Data/Data.zip')
+    #unzip
+    with zipfile.ZipFile('../Data/Data.zip', 'r') as zip_ref:
+        zip_ref.extractall('../Data/')
+    #os.remove(where_to_save+'BBBC007_v1_images.zip')
+
+'''
+# Single file download
+
+where_to_save = '../Data/'
+
+#create data directory
+if not os.path.exists(where_to_save):
+    os.makedirs(where_to_save)
+
+#import Klee painting
+#url = 'https://img.myswitzerland.com/671846/407'
+url = 'https://upload.wikimedia.org/wikipedia/commons/f/fd/%27%C3%9Cbermut_Exub%C3%A9rance%27_by_Paul_Klee%2C_1939.jpg'
+urllib.request.urlretrieve(url, where_to_save+'Klee.jpg')
+
+#import myoblast
+if not os.path.isfile(where_to_save+'myoblast.tif'):
+    url = 'https://cildata.crbs.ucsd.edu/media/images/13585/13585.tif' 
+    urllib.request.urlretrieve(url, where_to_save+'myoblast.tif')
+
+#import neuron
+if not os.path.isfile(where_to_save+'neuron.tif'):
+    url = 'https://cildata.crbs.ucsd.edu/media/images/809/809.tif'
+    urllib.request.urlretrieve(url, where_to_save+'neuron.tif')
+
+#import virus EM
+if not os.path.isfile(where_to_save+'virus_EM.tif'):
+    url = 'https://drive.google.com/uc?id=1wNjg6rihldcgR8_zRCGFYC8uLkxK1r9c'
+    urllib.request.urlretrieve(url, where_to_save+'virus_EM.tif')
+
+#import heart substack
+if not os.path.isfile(where_to_save+'cxcr4aMO2_290112_substack.tif'):
+    url = 'https://drive.google.com/uc?id=16bnFocL1jorjSOh3Uk6X_b_5Y6G3GHqF'
+    urllib.request.urlretrieve(url, where_to_save+'cxcr4aMO2_290112_substack.tif')
+
+#import channels
+if not os.path.isdir(where_to_save+'channels'):
+    os.makedirs(where_to_save+'channels')
+    url = 'https://drive.google.com/uc?id=1kNzXN_FkRflU4uNOpNfmpK8hUcJ1Dz6R'
+    urllib.request.urlretrieve(url, where_to_save+'channels/channels1.tif')
+    url = 'https://drive.google.com/uc?id=1OMBGdO3t_RvCIcmTLPX6zBfRiWt5KP3Z'
+    urllib.request.urlretrieve(url, where_to_save+'channels/channels2.tif')
+
+#import nuclei image
+if not os.path.isfile(where_to_save+'Image6AltFinal.tif'):
+    url = 'https://cildata.crbs.ucsd.edu/media/images/50658/50658.zip' 
+    urllib.request.urlretrieve(url, where_to_save+'50658.zip')
+    #unzip
+    with zipfile.ZipFile(where_to_save+'50658.zip', 'r') as zip_ref:
+        zip_ref.extractall(where_to_save)
+
+#import BBBC007
+if not os.path.isdir(where_to_save+'BBBC007_v1_images'):
+    url = 'https://data.broadinstitute.org/bbbc/BBBC007/BBBC007_v1_images.zip'
+    urllib.request.urlretrieve(url, where_to_save+'BBBC007_v1_images.zip')
+    #unzip
+    with zipfile.ZipFile(where_to_save+'BBBC007_v1_images.zip', 'r') as zip_ref:
+        zip_ref.extractall(where_to_save)
+    os.remove(where_to_save+'BBBC007_v1_images.zip')
+
+#import zebrafish embryo
+if not os.path.isdir(where_to_save+'30567'):
+    os.makedirs(where_to_save+'30567')
+    url = 'https://cildata.crbs.ucsd.edu/media/images/30567/30567.tif'  
+    urllib.request.urlretrieve(url, where_to_save+'30567/30567.tif')
+
+#download lsm example
+if not os.path.isfile(where_to_save+'hsp-17 translational tail z-stack raw.lsm'):
+    myfile = requests.get('https://zenodo.org/record/3594412/files/hsp-17%20translational%20tail%20z-stack%20raw.lsm?download=1', allow_redirects=True)
+    open(where_to_save+'hsp-17 translational tail z-stack raw.lsm', 'wb').write(myfile.content)
+
+#download mrc example
+if not os.path.isfile(where_to_save+'HeLa_H2B-PAGFP_01_12_R3D_D3D.dv'):
+    myfile = requests.get('https://zenodo.org/record/377035/files/HeLa_H2B-PAGFP_01_12_R3D_D3D.dv?download=1', allow_redirects=True)
+    open(where_to_save+'HeLa_H2B-PAGFP_01_12_R3D_D3D.dv', 'wb').write(myfile.content)
+'''