Open slidebook .sldy files in Python

The Institute of Cancer Research

Last update: May 4, 2022

Related tags

Miscellaneous slidebook-python

Overview

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)

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Comments

Fix loading of histogram data for slide scans

For some reason, slide scans fail when loading the histogram summaries. A fix to skip this step is added at https://github.com/instituteofcancerresearch/slidebook-python/blob/7bf6906dffd53d2b0326ab4ea0f81ce1e5c234e6/sld/slidebook.py#L18-L24

opened by adamltyson 0

Load timelapse images as single array using dask

Rather than loading N arrays into memory, concatenate using dask, e.g.:

import numpy as np
import dask.array as da
 
a = np.memmap('a.array', dtype='float64', mode='r', shape=( 5000,1000))
b = np.memmap('b.array', dtype='float64', mode='r', shape=(15000,1000))

c = da.concatenate([a, b], axis=0)

from https://stackoverflow.com/a/68138351

opened by adamltyson 1

Owner

The Institute of Cancer Research

The Institute of Cancer Research is making the discoveries that defeat cancer. We're the UK's top academic research centre, a postgrad college, and a charity.

GitHub

Open slidebook .sldy files in Python

Related tags

Overview

slidebook-python

To install

To use

To visualise in napari

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Comments

Fix loading of histogram data for slide scans

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