Are you looking to showcase your skills by building your own real-life microscopy workflow in a matter of hours? Then join the Microscopy Hackathon hosted by ZEISS Microscopy and Microsoft, together with their partners.

Hackathon Information

Why are We Organizing the Hackathon?

We are organizing the hackathon so you can join other hackers like you and engage in collaborative programming to rapidly develop microscopy workflow solutions. Ideally, the solutions would address challenges from your daily life, so that you create something that helps you in the future and potentially also many other microscopists. Of course, we expect you to have fun along the way.

When and Where Will It Take Place?

The hackathon is planned for 9 AM to 4 PM on the Sunday before M&M (August 5, 2018) at Hilton Baltimore Hotel, conveniently located right next to the M&M venue.


August 5, 2018
9:00 AM - 4:00 PM


Hilton Baltimore Hotel
Latrobe Room
401 West Pratt St.
Baltimore, MD 21201


Time Activity

8.30 AM - 9:00 AM


9:00 AM - 10:00 AM


10:00 AM - 3:00 PM

5 Hours of Hacking

3:00 PM - 4:00 PM

Presentations by hacking group to the jury

Food & Drinks

Snacks, lunch and soft drinks will be provided. Please let us know if you have any dietary restrictions or needs.


A 3-member jury will pick the winner based on the final presentations between 3 PM to 4 PM. Winners will be announced and prizes distributed either right after the event or on the following day on the exhibition floor at M&M. Arrangements are still being made and participants will be aptly notified.

There will be four sets of prizes each for the winning team, second place team, third place team, and all teams that finishes their workflows, respectively.

1st Prize: $250 gift card to each member of the team
2nd Prize: $100 gift card to each member of the team
3rd Prize: $50 gift card to each member of the team
All attendees will receive a ZEISS VR ONE headset upon completion of their solution!

The winning workflow will be showcased at the ZEISS Booth throughout the M&M exhibition event.



A total of no more than 30 hackers will be participating in the event, in groups of 3-5 people. The hackers are expected to have varying backgrounds; life sciences, materials sciences, computer sciences, and other related fields. All hackers must have coding skills in at least one scripting language, especially Python. Non-coders are accepted only if they bring a coding partner who helps with bringing their workflow to life. In fact, it is recommended to bring your own challenges or workflows that you'd like to build. If you don't have a specific workflow in mind you can always work on ideas proposed by your group members or the organizers. It is also recommended to bring your own data (images or other) as the data supplied by organizers may not be appropriate for the workflow you are building.

Hardware and Software

Please bring your own MacBook or Windows laptop pre-loaded with any required programming tools and libraries. You will be using Docker to create containers. Although, the containerization process is automated by the platform, it helps to install Docker on your system to make your offline testing easy. Docker installation is straightforward on a Windows 10 machine or Mac/Linux.

Docker for Windows
Docker for Mac

Please install the latest Git.

Platform Information

Why Did ZEISS Initiate the Efforts?

Microscopy helps advance our knowledge of the world, but even with great images, the journey towards gaining insights can be exceptionally challenging. Consider the amount of valuable research time wasted in converting file formats to work with fragmented pieces of software! Consider the pain trying to discover features in a bulky software! Consider the frustrations with sharing data and applications with your collaborators! ZEISS took initiative to address these challenges by creating a digital platform that enables researcher take control of every aspect of their microscopy workflows.

How Can the Digital Platform Help You?

The platform offers the infrastructure necessary for you to

  • define and execute end to end workflows, from microscope automation to getting results ready for publication
  • modularize your workflows for maximum re-usability
  • create your own software modules using any language of your choice, including Python, Java, and imageJ scripting
  • use cloud infrastructure to scale resources accordingly.
  • choose to share your work with the community or keep it private for personal use
  • connect with your peers to exchange knowledge

What Does the Platform Look Like?

The online platform will be demonstrated via webinar to accepted hackathon registrants on July 25th and 26th after which platform sign-up instructions will be distributed. Please pick a convenient day to attend the webinar while filling the hackathon registration form below.

Please contact Sreeni at sreenivas .bhattiprolu @zeiss .com for further details about the platform or hackathon.


Space is limited to the hackathon - only the first 30 qualified applicants will be accepted! Register today!