Open slidebook .sldy files in 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)
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.
The Institute of Cancer Research
Library to generate random strings from regular expressions.

Xeger Library to generate random strings from regular expressions. To install, type: pip install xeger To use, type: from xeger import Xeger

Colm O'Connor 101 Nov 15, 2022
ThnoolBox - A thneed is a multi-use versatile object

ThnoolBox Have you ever wanted a collection of bodged desktop apps that are Lorax themed ? No ? Sucks to suck I guess Apps & their downsides CalculaTh

pocoyo 1 Jan 21, 2022
App to get data from popular polish pages with job offers

Job board parser I written simple app to get me data from popular pages with job offers, because I wanted to knew immidietly if there is some new offe

0 Jan 04, 2022
Research on how Gboard Stickers work.

Google-Sticker-Mashup-Research Research on how Gboard Stickers work. Contribute Contributing is nice, and you will be listed below for contributing. C

Jeremiah 45 Oct 28, 2022
Allow you to create you own custom decentralize job management system.

ants Allow you to create you own custom decentralize job management system. Install $ git clone https://github.com/hvuhsg/ants.git Run monitor exampl

1 Feb 15, 2022
Protocol Buffers for the Rest of Us

Protocol Buffers for the Rest of Us Motivation protoletariat has one goal: fixing the broken imports for the Python code generated by protoc. Usage He

Phillip Cloud 76 Jan 04, 2023
My Dotfiles of Arco Linux

Arco-DotFiles My Dotfiles of Arco Linux Apps Used Htop LightDM lightdm-webkit2-greeter Alacritty Qtile Cava Spotify nitrogen neofetch Spicetify Thunar

$BlueDev5 6 Dec 11, 2022
A community based economy bot with python works only with python 3.7.8 as web3 requires cytoolz

A community based economy bot with python works only with python 3.7.8 as web3 requires cytoolz has some issues building with python 3.10

4 Jan 01, 2022
Python library for parsing Godot scene files

Godot Parser This is a python library for parsing Godot scene (.tscn) and resource (.tres) files. It's intended to make it easier to automate certain

Steven Arcangeli 30 Jan 04, 2023
Mixtaper - Web app to make mixtapes

Mixtaper A web app which allows you to input songs in the form of youtube links

suryansh 1 Feb 14, 2022
A tool to guide you for team selection based on mana and ruleset using your owned cards.

Splinterlands_Teams_Guide A tool to guide you for team selection based on mana and ruleset using your owned cards. Built With This project is built wi

Ruzaini Subri 3 Jul 30, 2022
Tenda D151 & D301 - Unauthenticated configuration download

Exploit Title: Tenda D151 & D301 - Unauthenticated configuration download (login included)

Ayoub 3 Jul 14, 2022
Banking management project using Tkinter GUI in python.

Bank-Management Banking management project using Tkinter GUI in python. Packages required Tkinter - Tkinter is the standard GUI library for Python. sq

Anjali Kumawat 7 Jul 03, 2022
Py4J enables Python programs to dynamically access arbitrary Java objects

Py4J Py4J enables Python programs running in a Python interpreter to dynamically access Java objects in a Java Virtual Machine. Methods are called as

Barthelemy Dagenais 1k Jan 02, 2023
A simple language for new programmers and a toy language ;)

Yell An extremely simple, yet powerful language for new programmers, as well as a toy language ;) Explore the docs » Report Bug · Request Feature Yell

Yell 4 Dec 28, 2021
TB Set color display - Add-on for Blender to set multiple objects and material Display Color at once.

TB_Set_color_display Add-on for Blender with operations to transfer name between object, data, materials and action names Set groups of object's or ma

1 Jun 01, 2022
Cairo-integer-types - A library for bitwise integer types (e.g. int64 or uint32) in Cairo, with a test suite

The Cairo bitwise integer library (cairo-bitwise-int v0.1.1) The Cairo smart tes

27 Sep 23, 2022
Fortnite StW Claimer for Daily Rewards, Research Points and free Llamas.

Fortnite Save the World Daily Reward, Research Points & free Llama Claimer This program allows you to claim Save the World Daily Reward, Research Poin

PRO100KatYT 27 Dec 22, 2022
A Google sheet which keeps track of the locations that want to visit and a price cutoff

FlightDeals Here's how the program works. First, I have a Google sheet which keeps track of the locations that I want to visit and a price cutoff. It

Lynne Munini 5 Nov 21, 2022
This repository contains all the data analytics projects that I've worked on in python.

93_Python_Data_Analytics_Projects This repository contains all the data analytics projects that I've worked on in python. No. Name 01 001_Cervical_Can

Milaan Parmar / Милан пармар / _米兰 帕尔马 267 Jan 06, 2023