WholeSlide for Education

An open medical education app for students around the world.

iPad mockup

1. TL;DR


To develop an open source1 iOS app for viewing high resolution virtual microscopy slides from open access content providers.

What are virtual slides?

Virtual slides are high resolution digital images of microscope slides. Think “Google Maps” for biopsies, brain anatomy, and blood work.

Who will use it?

Medical Students & Instructors, Clinicians, Researchers, Anatomists

How will they use it?

Instruction and reference – Teachers can organize their content or use it during class. Students can follow along or consult the app later for reference. More

Why open source1 it?

Lack of scalable market, resistance to open source, and very slow tech innovation in MedEd means this app would never be funded commercially

How can you help?

  • Individuals: Help us test and give us feedback.
  • Companies small and large: Sponsor a feature or server format.
  • Open access content providers: Let us index your content.
  • Everyone: Spread the word!

1The software license used is similar to that of software released by any major University. It is free to use for personal, research, and academic purposes. A standalone license is required for any clinical or commercial applications.

2. Jumpstarting medical education technology

I’ve created this project to develop an open source tablet-based virtual slide viewer for medical education. Such a product would rarely be funded as a research endeavor and has no scalable business model as a startup. This is a personal effort to put a usable tool into the hands of those that could teach with it and learn through it.

To start from nothing would require months of research and planning. Thankfully this won’t be necessary. In 2011, I released WholeSlide for iPad – a free application that allows medical students, educators, and clinicians to quickly access high resolution virtual microscopy images. Students can use the app to access virtual slide data from 10+ preselected sources including several brain atlases, digital pathology providers, and medical libraries. WholeSlide was a great start – but falls well short of being an effective tool for education.

With support from key sponsors and organizations, I will write a new version of WholeSlide taking advantage of the many improvements in modern iOS and Android development. It will be open source from day one, with each commit visible on a public github repository. To emphasize broader utility, I will engage early on with progressive academic institutions, agile industry partners, and philanthropic organizations interested in global medical education. The target audience will be US-based educators and students, with long-term targets aimed at international medical organizations and/or partnerships (e.g. UCSD’s Mepi project).

When complete (~ early 2014), I will publish a free, ad-free version of the application to the iTunes and Google Play store. The source code will remain available on github under an open license. Finally, I will compile a list of related tools and best practices for working with virtual microscopy slides targeted towards inexpensive but capable solutions for programs in developing nations.

3. The proposal

What will we build?

An open source iOS app for viewing high resolution virtual microscopy slides (link goes to github design docs).

We will start with a series of user stories and build from them a focused user interface. Unlike the original WholeSlide application, the new version will be built around a modular design with a goal of easy extensibility and customization.

Architecture Diagram (proposed)


The backend will support a range of virtual slide servers, image formats, and annotation formats. Browser modules will be built to support a range of content providers while a common virtual slide viewer will handle efficient image rendering.

Slide interaction modules will sit at the top of the stack providing ways to adjust the image properties, annotation details, or do something clever like link to an image search API.

What will it look like?

Aesthetically, we will use a simple palette and pay homage to the great Sublime Text 2 user interface. All textures and icons will be selected from Creative Commons or public domain sources.

basic view

Basic virtual slide view

The app will borrow heavily from tabbed web browsers & text editors – supporting reorganizable tabs, split-tab views, and means to link side-by-side views. This allows a user to bring up a course outline in the left view, while navigating a virtual slide in the right.

course view

Course view

All content in the design and development processes will be made available on github.com and released under an open license (derived from UCSD’s academic, non-commercial license).

How can you help?

  • If you’re an open access content provider, let us index your virtual slide list and course materials. Contact us via email and we’ll help you make your content available through the app. We greatly appreciate the effort put in to make high quality content available – we want to help it reach a broader audience.

  • If you’re a virtual slide server vendor, let us enable support for your server and annotation formats. By sponsoring the development, we’ll work with you to ensure first class support of one or more server formats as well as custom views for your content. Contact us and we’ll help figure out the best fit.

  • If you’re an educator, help us make the interface work as best as it can to provide an intuitive interface on top of your content. Become a beta tester to get early access to each build, with new releases pushed as features get added.

  • If you’re a student, help raise awareness for this project – pass the word on to your instructors or school administrators.

  • Philanthropists and Non-profits – Sponsor this project or a feature within. In addition to providing a tool for domestic (US-based) medical education – we’re actively looking at ways to get this app or an Android equivalent into the hands of medical students around the world.

Why open? Why not _______?

Commercial options were considered but decided against for the following reasons:

  • The market to support such an application is small.
  • The primary customers – medical students and researchers – are already loaded with debt.
  • By making the app open source and free, open-access content providers, server vendors, and academic institutions can come together to produce a single great thing rather than many single-purpose applications.

In short – this app is not being built with a sustainable business model in mind. It’s something that should exist even without a flush market to support it.

What happens after Version 1.0.0 is released?

I will continue to work on improving the code base and add support for more slide sources. I will maintain a searchable index for content providers to populate and access through the app.

4. Development timeline

Milestone I – Start September 15, Complete by October 30

WholeSlide code base refresh and initial release. Github site is populated and partners can start adding features in the form of GH issues.

Milestone II – Start November 1, Complete by December 30

Feature additions and continued testing. Periodic releases (timeline TBD) as new features and data sources come online

Milestone III – January 1, 2014

First public release. App goes live on store for free.

5. Useful links

The WholeSlide Blog

Periodic updates about the project will be located here: http://wholeslide.com/blog/

Github repositories

General development, design, and utilities – https://github.com/wholeslide/wholeslidesupport

Wiki used for documentation – https://github.com/wholeslide/wholeslidesupport/wiki

Primary app repository – https://github.com/wholeslide/openslideviewer

Other sites

Rich Stoner’s personal blog – richstoner.github.io

FigureZero open source project – https://github.com/wholeslide/figurezero