A 3D Slicer Extension to view data from the flywheel heirarchy

Related tags

Miscellaneouspython3d-slicer-extensionslicer-ex
Overview

flywheel-connect

A 3D Slicer Extension to view, select, and download images from a Flywheel instance to 3D Slicer and storing Slicer outputs back to Flywheel.

Flywheel is a comprehensive data management solutions for life sciences and imaging research. More details at https://flywheel.io/.

The Flywheel Connect 3D Slicer Extension is now in the 3D Slicer Extension Catalog and available through the 3D Slicer Extensions Manager for direct installation.

Usage Instructions

  1. Install 3D Slicer and the Flywheel extension as described here.

  2. Navigate to flywheel-connect under the Modules drop-down box. Select Extension

  3. To access the Flywheel container hierarchy first enter your Flywheel api-key and press "connect". If you have logged in with the Flywheel CLI (Command-Line-Interface), the cached Flywheel api-key can be used without entering a new one.

  4. Navigate to the desired Acquisition in the Container Hierarchy Tree for a particular project.

  5. By clicking on a file or files in the "Files" of a container, they can be loaded into 3D Slicer if they are images or models of the 3D Slicer Supported Data Formats. Compressed archives of DICOMs are also supported, if they are labeled as such in Flywheel.

  6. By clicking on a container, slicer-derived files can be uploaded to Flywheel as

    • Files under a selected container
    • Files for a new Analysis object under a selected container.

File Management

Files will be cached to the flywheelIO/ directory of the users home directory. This is default and can be changed. If caching files is not desired, uncheck "Cache Images". This will delete all files in the cache between downloads.

Interface Overview

The interface is shown below. Notable areas are commented on:

Tree View

  • A) The API-Key can be entered here. Or the cached API-Key will be used from a previous fw login {API-KEY} command. When connecting to a Flywheel instance all data will be cleared from 3D Slicer to prevent invalid data references between Flywheel instances. If there is no previously cached login--or the supplied API-Key is invalid--an error dialog is displayed.
  • B) Default disk cache.
  • C) If unchecked, the cache will be cleared between downloads.
  • D) Select Box for Groups. This will "cascade" selections for the first project, if it exists.
  • E) Select Box for Projects. The selected project will clear and repopulate the tree. If no project exists, the tree is not enabled.
  • F) Analyses objects are not automatically cached. Double-clicking will load all Analysis.
  • G) Files that are cached will have a green "badge". Right-clicking on selected files will enable them to be cached. Some downloads are large.
  • H) Load all selected files. Files that are Slicer-supported data formats (Images and Models) will be loaded. This will only be enabled if files are selected.
  • I) Upload derived files to Flywheel Analysis or Container files. This will only be enabled if a single valid Flywheel Container is selected.
  • H) If checked, indicates that derived files should be uploaded to Flywheel as Analysis output under the selected Container.
You might also like...
An extension module to make reaction based menus with disnake

disnake-ext-menus An experimental extension menu that makes working with reaction menus a bit easier. Installing python -m pip install -U disnake-ext-

null 1 Nov 25, 2021
Functional collections extension functions for Python

pyfuncol pyfuncol Installation Usage API Documentation Compatibility Contributing License A Python functional collections library. It extends collecti

Andrea Veneziano 32 Nov 16, 2022
Gaia: a chrome extension that curates environmental news of a company
Gaia: a chrome extension that curates environmental news of a company

Gaia - Gaia: Your Environment News Curator Call for Code 2021 Gaia: a chrome extension that curates environmental news of a company Explore the docs »

null 4 Mar 19, 2022
A ULauncher/Albert extension that supports currency, units and date time conversion, as well as a calculator that supports complex numbers and functions.
A ULauncher/Albert extension that supports currency, units and date time conversion, as well as a calculator that supports complex numbers and functions.

Ulauncher/Albert Calculate Anything Ulauncher/Albert Calculate Anything is an extension for Ulauncher and Albert to calculate things like currency, ti

tchar 67 Jan 1, 2023
An Embedded Linux Project Build and Compile Tool -- An Bitbake UI Extension
An Embedded Linux Project Build and Compile Tool -- An Bitbake UI Extension

Dianshao - An Embedded Linux Project Build and Compile Tool

null 0 Mar 27, 2022
Nuclei - Burp Extension allows to run nuclei scanner directly from burp and transforms json results into the issues
Nuclei - Burp Extension allows to run nuclei scanner directly from burp and transforms json results into the issues

Nuclei - Burp Extension Simple extension that allows to run nuclei scanner directly from burp and transforms json results into the issues. Installatio

null 106 Dec 22, 2022
An addin for Autodesk Fusion 360 that lets you view your design in a Looking Glass Portrait 3D display

An addin for Autodesk Fusion 360 that lets you view your design in a Looking Glass Portrait 3D display

Brian Peiris 12 Nov 2, 2022
A Lego Mindstorm robot for dealing out cards based on a birds-eye view of a poker table and given ArUco fiducial tags.

A Lego Mindstorm robot for dealing out cards based on a birds-eye view of a poker table and given ArUco fiducial tags.

null 4 Dec 6, 2021
Direct Multi-view Multi-person 3D Human Pose Estimation
Direct Multi-view Multi-person 3D Human Pose Estimation

Implementation of NeurIPS-2021 paper: Direct Multi-view Multi-person 3D Human Pose Estimation [paper] [video-YouTube, video-Bilibili] [slides] This is

Sea AI Lab 253 Jan 5, 2023
Comments
  • Ad extension to Slicer extension manager

    Ad extension to Slicer extension manager

    I've come across this extension now. Nice work!

    You can make this extension available for Slicer users by submitting it to the extensions index.

    This would increase its visibility for Slicer users and make installation much easier.

    opened by lassoan 3
  • GEAR-2613/Correct_Self_Test_For_CDash_hosted_CI

    GEAR-2613/Correct_Self_Test_For_CDash_hosted_CI

    This PR corrects for the failing tests that are reported at the CDash-hosted CI for 3D Slicer: https://slicer.cdash.org/index.php?project=SlicerStable&filtercount=1&showfilters=1&field1=buildname&compare1=63&value1=flywheel_connect

    opened by joshicola 0
  • Gear_2402/add collections as entry point

    Gear_2402/add collections as entry point

    Modifications present the user with radio buttons to choose between:

    • Browsing Groups and Projects
    • Browsing Collections

    Further modifications were performed to ensure:

    • Collections do not list Analyses folders
    • Flywheel-Connect cannot save to Analyses under Collections
    • Files from Collections are cached and referenced as needed.
    opened by joshicola 0
Releases(1.1.0)
Owner
GitHub Repository
Python interface to IEX and IEX cloud APIs

Python interface to IEX Cloud Referral Please subscribe to IEX Cloud using this referral code. Getting Started Install Install from pip pip install py

IEX Cloud 41 Dec 21, 2022
A simple python script where the user inputs the current ingredients they have in their kitchen into ingredients.txt

A simple python script where the user inputs the current ingredients they have in their kitchen into ingredients.txt and then runs the main.py script, and it will output what recipes can be created b

Jordan Leich 3 Nov 02, 2022
Bots in moderation and a game (for now)

Tutorial: come far funzionare il bot e durarlo per 24/7 (o quasi...) Ci sono 17 passi per seguire: Andare sul sito Replit https://replit.com/ Vedrete

ZacyKing 1 Dec 27, 2021
The semi-complete teardown of Cosmo's Cosmic Adventure.

The semi-complete teardown of Cosmo's Cosmic Adventure.

Scott Smitelli 10 Dec 02, 2022
This is a practice on Airflow, which is building virtual env, installing Airflow and constructing data pipeline (DAGs)

airflow-test This is a practice on Airflow, which is Builing virtualbox env and setting Airflow on that env Installing Airflow using python virtual en

Jaeyoung 1 Nov 01, 2021
DNA Storage Simulator that analyzes and simulates DNA storage

DNA Storage Simulator This monorepository contains code for a research project by Mayank Keoliya and supervised by Djordje Jevdjic, that analyzes and

Mayank Keoliya 3 Sep 25, 2022
A python package to manage the stored receiver-side Strain Green's Tensor (SGT) database of 3D background models and able to generate Green's function and synthetic waveform

A python package to manage the stored receiver-side Strain Green's Tensor (SGT) database of 3D background models and able to generate Green's function and synthetic waveform

Liang Ding 7 Dec 14, 2022
This repository contains a lot of short scripting programs implemented both in Python (Flask) and TypeScript (NodeJS).

fast-scripts This repository contains a lot of short scripting programs implemented both in Python (Flask) and TypeScript (NodeJS). In python These wi

Nahum Maurice 3 Dec 10, 2022
Expression interpreter written in Python

Calc Interpreter An interpreter modeled after a calculator implemented in Python 3. The program currently only supports basic mathematical expressions

1 Oct 17, 2021
Hook and simulate global keyboard events on Windows and Linux.

keyboard Take full control of your keyboard with this small Python library. Hook global events, register hotkeys, simulate key presses and much more.

BoppreH 3.2k Jan 01, 2023
Flow control is the order in which statements or blocks of code are executed at runtime based on a condition. Learn Conditional statements, Iterative statements, and Transfer statements

03_Python_Flow_Control Introduction 👋 The control flow statements are an essential part of the Python programming language. A control flow statement

Milaan Parmar / Милан пармар / _米兰 帕尔马 209 Oct 31, 2022
A simple package for interacting with the 9kw.eu anti-captcha service.

Welcome to captcha9kw’s documentation! captcha9kw is a smallish Python package for making use of the 9kw.eu services, including solving of interactive

2 Feb 26, 2022
An integrated library for checking email if it is registered on social media

An integrated library for checking email if it is registered on social media

Sidra ELEzz 13 Dec 08, 2022
a bit of my project :) and I use some of them for my school lesson or study for an exam! but some of them just for myself.

Handy Project a bit of my project :) and I use some of them for my school lesson or study for an exam! but some of them just for myself. the handy pro

amirkasra esmaeilian 13 Jul 05, 2021
Always fill your package requirements without the user having to do anything! Simple and easy!

WSL Should now work always-fill-reqs-python3 Always fill your package requirements without the user having to do anything! Simple and easy! Supported

Hashm 7 Jan 19, 2022
Install packages with pip as if you were in the past!

A PyPI time machine Do you wish you could just install packages with pip as if you were at some fixed date in the past? If so, the PyPI time machine i

Thomas Robitaille 51 Jan 09, 2023
oracle arm registration script.

oracle_arm oracle arm registration script. 乌龟壳刷ARM脚本 本脚本优点 简单,主机配置好oci，然后下载main.tf即可，不用自己获取各种参数。 运行环境配置 本简单脚本使用python3编写，请自行配置好python3环境和requests库。（高版

test1234455 419 Jan 01, 2023
More granular intermediaries for legacy Minecraft versions

Orinthe/Intermediary mappings This repository contains the match information between different versions of Minecraft created by the Orinthe project, a

4 Jan 11, 2022
A plugin for poetry that allows you to execute scripts defined in your pyproject.toml, just like you can in npm or pipenv

poetry-exec-plugin A plugin for poetry that allows you to execute scripts defined in your pyproject.toml, just like you can in npm or pipenv Installat

38 Jan 06, 2023
ThinkPHP全日志扫描工具，命令行版和BurpSuite插件版

ThinkPHP3和5日志扫描工具，提供命令行版和BurpSuite插件版，尽可能全的发掘网站日志信息 命令行版 安装 git clone https://github.com/r3change/TPLogScan.git cd TPLogScan/ pip install -r requireme

119 Dec 27, 2022