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Welcome to BIOP-desktop
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index.md

| Demo | Installation | Build | Run | FAQ |

Acknowledgements

This whole project was possible thanks to the previous work of the renku team (renku-desktop) and the support of the RCP and SV IT teams, EPFL.

Introduction

The BIOP-desktop is a Versioned Computer with software pre-installed and pre-configured so you can focus on your analysis (and not on the installation).

desktop-screeshot

The BIOP-desktop is a Docker image that you can simply pull and run (and optionnaly build yourself)

BIOP-desktop_Fresk ( enlarge image )

The BIOP-desktop is :

Developper Point of View IT Point of View Users Point of View
a Docker image that you can build using multi-stage a Docker image that you can simply pull and run a Computer with "everything" installed and running!

What is a Versioned Computer?

By Versioned Computer, we mean a computer in which every software is set, making it possible to reproduce the same environment at any time.

Making use of the Docker images, we can create a Versioned Computer that is reproducible, shareable, and open. We make use of multi-stage build to ease building and versionning. Indeed we can build a new image, changing a single component and keeping the rest of the image unchanged, if needed.

What is a Versioned Computer for?

A Versioned Computer is useful for:

  • Focusing on your analysis: you don't have to worry about installing and configuring software.
  • Reproducibility: you can reproduce your analysis at any time, even years later.
  • Collaboration: you can share your analysis with your collaborators, and they can reproduce it.
  • Teaching: you can share your analysis with your students, and they can reproduce it.
  • Publication: you can share your analysis with the reviewers, and they can reproduce it.
  • Open Science: you can share your analysis with the world, and they can reproduce it.

Why did we create the BIOP-desktop?

We created the BIOP-desktop to help you focus on your analysis, and not on the installation and configuration of software. BUT we created it also because we need it ourself!

As a core facility, we give courses on image processing and image analysis and practical training on software we create workflows and we wanted a solution that can work locally (on our workstations 12-32 cores, 128-512GB RAM, 12-24GB GPU) and remotely (cluster with 80GB-GPU).

Mainting the software on all our workstation is a burden and we wanted a solution that can ease this task.

BIOP-desktop installed software

Software Description Notes
ABBA Aligning Big Brains & Atlases including : elastix & transformix, DeepSlice, ...
cellprofiler Open-source software designed to enable biologists to quantitatively measure phenotypes from thousands of images automatically.
cellpose An anatomical segmentation algorithm, to detect nucleus, cells, and much more ! and omnipose too!
devbio-napari The Fijiest way to do image analysis in Python
EMPanADA DNN to segment mitochondria in EM images
Fiji A “batteries-included” ImageJ update sites : clij, stardist, ptbiop , ilastik …
ilastik (GPU) Interactive learning and segmentation toolkit GPU version
inkscape Vectoriel drawing (and more!) with inkscape-imagej-panel plugins
QuPath Digital Pathology with some extensions : cellpose, SAM , Warpy , StarDist...
StarDist Object Detection with Star-convex Shapes