Who We Are

Our VC firm has called us “hot-pink-haired techno punks,” which conveys a part of our culture (we are out of office en masse during Burning Man), but not all of us look like villains from Captain Planet. We’re united by intellectual curiosity and a desire to further the progress of biology. We have monthly talks on intellectual subjects, ranging from histology to optics to polymer physics. The company has several patents and scientific publications, and we’ve trademarked the term Squishware™ for one of our company departments.

For more information, see our Mission and History pages.


3Scan Galactic Headquarters
2122 Bryant St.
San Francisco, CA 94110 [Mission district]


Company Size
~20 employees, ~7 of whom on the software team. About three of those work on the analysis software stack, which only interacts tangentially with the acquisition stack.


Hours and Vacations
Flexible. 3Scan has a communications policy, not a vacation policy. You’ll be expected to be here from around 10AM – 5PM each day in general to coordinate with the rest of us, but working from home and vacations are left to your discretion. It’s your responsibility to get your work done, schedule your own time off, and communicate with your colleagues about when you’ll be out.


Funding Status
We raised $7.1MM in a Series A, led by Lux Capital, in late 2014. We also have non-negligible revenue from imaging contracts.




Senior Software Developer / Acquisition Team Lead

Seeking software developer for web-controlled brain-slicing robots:

You will direct the acquisition of tera-voxels per day of imagery data for science and profit. You must have a strong background in thick-client web development, and you must not be afraid of getting your hands dirty interfacing with robotics hardware and distributed computing. We’re less concerned with the individual skills or experience that you possess, and more interested in your ability to learn quickly and manage heterogeneous codebases like ours. We’re transitioning some developers over to the analysis software stack, so you will be taking over the development of the acquisition stack, with about three other developers contributing some of their time to this project with you.


The system you’ll be in charge of:
Meteor servers provide the control interfaces for the microscopes, as well as a google-maps-style viewer for the resulting imagery. The robots themselves and our local processing and storage cluster all run Python 3. The local machines pass the data around using zeroMQ as they do some inline processing, then store it in a series of RAID arrays, which we use as a local cache that we continuously upload to Amazon S3.

For more information, contact matt@3scan.com.


Software Developer / Web Lead

Face it, your web development job is boring.


Come join us at 3scan and put those hard-won coding skills toward revolutionizing our understanding of biology. At 3Scan, our robots use diamond knives and advanced optics to collect teravoxels per day of imagery data for science and profit. We use web services in several critical portions of our stack, and we need you to take over development of those services and create some new ones from scratch.


Required skills:
  • Fluency in JavaScript (we use Meteor with ES2015)
  • Comfort with Python for API and backend support
  • Ability to develop user interfaces and iterate based on feedback from users and the sales team


Bonus skills and experience:
  • AWS ecosystem, especially S3 and EC2
  • MongoDB
  • Distributed systems
  • Robotics
  • 3D Graphics and data visualization


The systems you’ll be working with:
You’ll take over development of our Meteor servers that provide the control interfaces for the microscopes, a google-maps-style viewer for the resulting imagery, and various metadata and log management interfaces. You’ll play a major role in creating novel web-driven tools to visualize and annotate massive amounts of volumetric data. Finally, you’ll lead the development of a portal for customers to manage their billing, create and monitor their projects with us, and download and visualize the resulting data.

For more information, contact matt@3scan.com.


Image Processing Engineer
At 3Scan, we routinely collect multi-terabyte data sets, and we need help building tooling, pipelines, and algorithms capable of interacting with data at that scale. There are a number of places that this data will take you—beginning with in-house machine optimization and branching out to having a direct impact on human medical research and decision making. If this excites you, we would love to talk about how to take our image processing to the next level.  


Core requirements:
  • Python—Relevant experience with numpy, scipy, openCV, scikit-image, and similar.
  • Image Processing Experience
  • Computational Geometry—Creating/managing algorithms around 3d data and associated representations


  • Spark / HPC computing experience
  • Experience with microscopy/MRI/CT or any voxel based modality
  • Experience with cloud compute environments
  • Experience with ConvNet
  • Any knowledge of Biology


For more information, contact matt@3scan.com.


Process Optimization Engineer
We have taken over a half-million slices since we started at 3scan.  Each slice has hundreds of control parameters and dozens of metrics related to resulting image quality. At present, it is largely the responsibility of a human operator to ensure the smooth sailing of our microscopes through this complex phase-space, but as production and scanning demands increase we need to make better decisions day to day and moment to moment. Your role will initially be the analysis of collected process data and evolve into a role guiding future acquisition and control.


Core Requirements:
  • Python—Relevant experience with numpy, scipy, pandas, scikit-learn and similar.
  • Hardware experience—With image sensors, control systems, microcontrollers, and data acquisition 
  • Basic knowledge of process engineering stratagies—Six-Sigma, takt time


  • Image processing experience


For more information, contact matt@3scan.com.



3scan is always looking for academic and industry researchers who want to tackle tough problems in 3d microscopy.


To encourage community growth we offer:

  • Free trial scans – Mail us samples, and we will produce demo data and reconstructions to explore possibilities.
  • Grant writing help –  We are willing to work with researchers to incorporate KESM technology into existing workflow.
  • Free data hosting – For any and all publicly available KESM data sets.


For more information, contact matt@3scan.com.


Interns and Consultants:

We are actively looking for a few good interns. Spend the summer in San Francisco living the Mission District lifestyle and working with a Bay Area startup on tough problems ranging from machine learning to precision mechanical design.


Skills we are looking for:

  • Open-Source, collaborative minded individuals
  • Experience with fluorescence microscopy and optical design
  • Image processing, big data, and machine learning skills
  • Optical, Mechanical, and Electronics Hackers


For more information, contact matt@3scan.com.

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