def analyze(conn, plate, pipeline):
warnings.filterwarnings('ignore')
print("analyzing...")
# Set Cell Output Directory
new_output_directory = os.path.normcase(tempfile.mkdtemp())
cpprefs.set_default_output_directory(new_output_directory)
wells = list(plate.listChildren())
wells = wells[0:5] # use the first 5 wells
for count, well in enumerate(wells):
# Load a single Image per Well
image = well.getImage(0)
print(image.getName())
pixels = image.getPrimaryPixels()
size_c = image.getSizeC()
# For each Image in OMERO, we copy pipeline and inject image modules
pipeline_copy = pipeline.copy()
# Inject image for each Channel (pipeline only handles 2 channels)
for c in range(0, size_c):
plane = pixels.getPlane(0, c, 0)
image_name = image.getName()
# Name of the channel expected in the pipeline
if c == 0:
image_name = 'OrigBlue'
if c == 1:
image_name = 'OrigGreen'
inject_image_module = InjectImage(image_name, plane)
inject_image_module.set_module_num(1)
pipeline_copy.add_module(inject_image_module)
pipeline_copy.run()
# Results obtained as CSV from Cell Profiler
path = new_output_directory + '/Nuclei.csv'
save_results(conn, path, image)
print("analysis done")
def analyze(plate, pipeline):
warnings.filterwarnings('ignore')
print("analyzing...")
# Set Cell Output Directory
new_output_directory = os.path.normcase(tempfile.mkdtemp())
cpprefs.set_default_output_directory(new_output_directory)
files = list()
wells = list(plate.listChildren())
wells = wells[0:5] # use the first 5 wells
plate_id = plate.getId()
for count, well in enumerate(wells):
# Load a single Image per Well
image = well.getImage(0)
print(image.getName())
data = load_dask_array_from_s3(plate_id,
(well.row + 1) * (well.column + 1) - 1)
size_c = image.getSizeC()
# For each Image in OMERO, we copy pipeline and inject image modules
pipeline_copy = pipeline.copy()
# Inject image for each Channel (pipeline only handles 2 channels)
for c in range(0, size_c):
plane = data[0, c, 0, :, :]
image_name = image.getName()
# Name of the channel expected in the pipeline
if c == 0:
image_name = 'OrigBlue'
if c == 1:
image_name = 'OrigGreen'
inject_image_module = InjectImage(image_name, plane)
inject_image_module.set_module_num(1)
pipeline_copy.add_module(inject_image_module)
pipeline_copy.run()
# Results obtained as CSV from Cell Profiler
path = new_output_directory + '/Nuclei.csv'
files.append(path)
print("analysis done")
return files
