Open neuromusic opened 5 years ago
Note: the "rendering imagestacks in holoviews" part of this may be easier with #1472
after @shanaxel42 reminded me of #1136, I'm closing #1472
one barrier to using holoviews with the imagestack xarray is that x and y don't have coordinates.
this works, however...
from starfish import Experiment
e = Experiment.from_json('https://d2z4zivcmlmaj1.cloudfront.net/ISS/mouse_vs_human/experiment.json')
imgs = e.fov().get_image('primary')
import holoviews as hv
hv.extension('matplotlib')
imgs.xarray.name = 'primary'
ds = hv.Dataset(imgs.xarray.set_index(x='xc',y='yc',z='zc'))
ds.to(hv.Image,['x','y'])
holoviews/bokeh offers interactive visualization of n-dimensional xarray datasets, making them an ideal way to interactively explore image stacks
advantages: