Widget to browse LIF scenes

browse_LIF.py

#%%
from aicsimageio import AICSImage
import napari
import dask.array as da
import numpy as np
from vispy.color import Colormap
import os
from qtpy.QtWidgets import QListWidget
from qtpy.QtCore import Qt

#%%
# Load data from LIF into a dask stack
img = AICSImage(
    os.path.expanduser("~/Documents/Leica DMi8/20210428/20210428_24w_L929_Ho_B2C3.lif"),
    reconstruct_mosaic=False,
)

#%%
# get pixel sizes (this is px/micron)
# 1/img.physical_pixel_sizes.X was needed before AICSI 4.10 now it's fixed!
microns_per_pixel = [img.physical_pixel_sizes.X, img.physical_pixel_sizes.Y]
# User Napari to view the stack of ROIs
I_Blueish = Colormap([[1, 1, 1], [0, 0.4, 1], [0, 0, 0]])


#%%
def open_scene(item):
    scene = item.text()
    img.set_scene(scene)
    viewer.add_image(
        img.get_image_dask_data("CZYX"),
        name=scene,
        colormap=("I Blueish", I_Blueish),
        scale=microns_per_pixel,
    )


#%%
# Cache dask stuff, based on @TalleyJLambert in napari zulip
from napari.utils import resize_dask_cache

cache = resize_dask_cache()
# Widget based on @sofroniewn https://github.com/sofroniewn/image-demos/blob/b39128d708cbb88902bd91ac383da3772c51eb64/examples/rxrx19_browser.py
viewer = napari.Viewer()
list_widget = QListWidget()
for scene in img.scenes:
    list_widget.addItem(scene)
list_widget.currentItemChanged.connect(open_scene)
viewer.window.add_dock_widget([list_widget], area="right")


# %%