Work in progress
slidebook-python
Open slidebook .sldy files in Python
To install
slidebook-python requires Python >= 3.9
pip install slidebook-python
To use
from sld import SlideBook
sld = SlideBook("/path/to/file.sldy")
# How many acquisitions
print(sld.number_acquisitions)
# 4
# How many channels in first acquisition
print(sld.images[0].num_channels)
# Get data from channel 0 of the second acquisition
data = sld.images[1].data["ch_0"]
To visualise in napari
N.B. napari plugin is in development
import napari
import numpy as np
from sld import SlideBook
sld = SlideBook("/path/to/file.sldy")
viewer = napari.Viewer()
viewer.add_image((np.squeeze(sld.images[0].data["ch_0"])), name="Channel 0")
viewer.add_image((np.squeeze(sld.images[0].data["ch_1"])), name="Channel 1")
napari.run()
By default, Slidebook will not load image data into memory. To force this, use mmap_mode=None:
sld = SlideBook("/path/to/file.sldy", mmap_mode=None)
