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
The fastest way to copy to (not from) high speed flash storage.

FastestCopy The fastest way to copy to (not from) high speed flash storage. This is about 3-6x faster than file copy on explorer.exe to usb flash driv

Derek Frombach 0 Nov 03, 2021
The little-endian version of MessagePack

MessagePackEL This is the little-endian version of MessagePack, except the endianness is different, the rest is exactly the same as MessagePack. C lib

dukelec 9 May 13, 2022
vFuzzer is a tool developed for fuzzing buffer overflows, For now, It can be used for fuzzing plain vanilla stack based buffer overflows

vFuzzer vFuzzer is a tool developed for fuzzing buffer overflows, For now, It can be used for fuzzing plain vanilla stack based buffer overflows, The

Vedant Bhalgama 5 Nov 12, 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
Python template for Advent of Code event

Advent of Code Python Starter A tamplate for Advent of Code write in Python. Usage The project use poetry for project manager. Clone this repository a

Leonardo Gago 6 Dec 31, 2022
Python Create Your Own Tool Series

Python Create Your Own Tool Series Hey there! This is an additional Github repository that contains the final product files for each video in my Youtu

Joe Helle 21 Dec 02, 2022
Pypot ⚙️ A Python library for Dynamixel motor control

Pypot ⚙️ A Python library for Dynamixel motor control Pypot is a cross-platform Python library making it easy and fast to control custom robots based

Poppy Project 238 Nov 21, 2022
Sudo type me a payload

payloadSecretary Sudo type me a payload Have you ever found yourself having to perform a test, and a client has provided you with a VM inside a VDI in

7 Jul 21, 2022
a simple proof system I made to learn math without any mistakes

math_up a simple proof system I made to learn math without any mistakes 0. Short Introduction test yourself, enjoy your math! math_up is an NBG-based,

양현우 5 Jun 04, 2021
A tool for fixing inconsistent timestamp metadata (atime, ctime, and mtime).

Mtime Fixer Mtime Fixer is a tool for fixing inconsistent timestamp metadata (atime, ctime, and mtime). Sometimes timestamp metadata of folders are in

Halit Şimşek 2 Jan 11, 2022
The only purpose of a byte-sized application is to help you create .desktop entry files for downloaded applications.

Turtle 🐢 The only purpose of a byte-sized application is to help you create .desktop entry files for downloaded applications. As of usual with elemen

TenderOwl 14 Dec 29, 2022
A powerful and user-friendly binary analysis platform!

angr angr is a platform-agnostic binary analysis framework. It is brought to you by the Computer Security Lab at UC Santa Barbara, SEFCOM at Arizona S

6.3k Jan 02, 2023
In this project we will be using OpenCV to virtually drag a rectangle and drop it at a different location. It will be further used for Virtual Mouse.

Virtual Drag & Drog using OpenCV In this project we will be using OpenCV to virtually drag a rectangle and drop it at a different location. It will be

Hassan Shahzad 5 Sep 27, 2021
Online-update est un programme python permettant de mettre a jour des dossier et de fichier depuis une adresse web.

Démarrage rapide Online-update est un programme python permettant de mettre a jour des dossier et de fichier depuis une adresse web. Mode préconfiguré

pf4 2 Nov 26, 2021
This code extracts line width of phonons from specular energy density (SED) calculated with LAMMPS.

This code extracts line width of phonons from specular energy density (SED) calculated with LAMMPS.

Masato Ohnishi 3 Jun 15, 2022
Mannaggia is a python application to praise or more likely to curse the saints

Mannaggia-py 👼 Remember Mannaggia? This is a Python remake of it, with new features. mannaggia is a python application to praise or more likely to cu

Christian Visintin 9 Aug 12, 2022
Python data loader for Solar Orbiter's (SolO) Energetic Particle Detector (EPD).

Data loader (and downloader) for Solar Orbiter/EPD energetic charged particle sensors EPT, HET, and STEP. Supports level 2 and low latency data provided by ESA's Solar Orbiter Archive.

Jan Gieseler 9 Dec 16, 2022
ToDo - A simple bot to keep track of things you need to do

ToDo A simple bot to keep track of things you need to do. Installation You will

3 Sep 18, 2022
An OBS script to fuze files together

OBS TEXT FUZE Fuze text files and inject the output into a text source. The Index file directory should be a list of file directorys for the text file

SuperZooper3 1 Dec 27, 2021
Secret santa is a fun and easy way to get together with your friends and/or family with a gift for them.

Vaccine Validator Tool to validate domestic New Zealand vaccine passes Create a new virtual environment: python3 -m venv ./venv Activate virtual envi

2 Dec 06, 2021