starfish_blob_2D_bug.py

import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import os

from starfish import Experiment, FieldOfView, ImageStack, display
from starfish.core.spots.DecodeSpots.trace_builders import build_traces_sequential
from starfish.spots import AssignTargets, FindSpots, DecodeSpots
from starfish.image import ApplyTransform, LearnTransform, Filter
from starfish.types import Axes, Levels
from starfish.util.plot import diagnose_registration, imshow_plane, intensity_histogram, overlay_spot_calls

# load data
experiment = Experiment.from_json('https://d26bikfyahveg8.cloudfront.net/RNAScope/formatted/experiment.json')
imgs = experiment["fov_000"].get_image(FieldOfView.PRIMARY_IMAGES)
dapi = experiment["fov_000"].get_image('nuclei')

# register images
learn_translation = LearnTransform.Translation(reference_stack=dapi.sel({Axes.ROUND: 0}), axes=Axes.ROUND, upsampling=1000)
transforms_list = learn_translation.run(dapi)
registered_imgs = warp.run(imgs, transforms_list=transforms_list, in_place=False)

# white tophat filter
whitetophat = Filter.WhiteTophat(masking_radius=2, is_volume=False)
wth_imgs = whitetophat.run(registered_imgs, in_place=False)

# define blob detector for 2D images
bd = FindSpots.BlobDetector(
    min_sigma=0.5,
    max_sigma=2,
    num_sigma=9,
    threshold=0.2,
    is_volume=False,
    measurement_type='mean',
)

# run blob detector without reference_image
bd_spots = bd.run(image_stack=wth_imgs)