Main Menu (Mobile)- Block

Main Menu - Block

Scientific Computing Software

janelia7_blocks-janelia7_secondary_menu | block
janelia7_blocks-janelia7_fake_breadcrumb | block
Support Teams / Scientific Computing Software
janelia7_blocks-janelia7_support_team_header | block

What We Do

Scientific Computing Software works closely with Janelia's labs, project teams, and shared resources. We can help with research and engineering tasks, providing everything from help with a quick question to full software life cycle support. You can find a recent recording that tries to summarize our department on YouTube.

node:body | entity_field


Our team’s software skills span a broad range of

  • programming languages (e.g. Java, Python, Julia, C++, Matlab)
  • extendable applications (e.g. Fiji, Napari, BigDataViewer, Neuroglancer)
  • frameworks (e.g. NumPy/SciPy, ImgLib2, PyTorch, Spark, Dask)
  • cloud & cluster technologies (e.g. storage and distributed compute on Amazon Web Services, Google Cloud & Janelia cluster, containerization)
  • databases (e.g. MySQL, MongoDB).

In addition to software skills, our team has deep domain knowledge in image processing, machine learning, (large) data handling, electron and light microscopy, instrument control, 3D graphics & visualization as well as bioformatics & transcriptomics and many of us have worked in biology, so we can efficiently work with experimentalists and computer scientists! Almost half of our team members have earned PhDs, in areas including computer engineering, electrical engineering, physics, biology, biochemistry, and computational neuroscience. To have an overview and/or find a good person to talk to we maintain a skills matrix available to internal users.

Our Goals

It is very important for us to identify opportunities for code reuse, reducing development overhead and support costs across Janelia. To achieve this we are strong proponents of open science and for example teamed up with the Computation & Theory research area (C&T) to create the Open Science Software Initiative. Additionally, most of our software is open source and available via GitHub.

We strive to be an active part of Janelia's scientific community and you will see us attending presentations and interest groups. Additionally, SciComp Software holds weekly office hours. We also have a series of Scientific Computing Interest Groups that are open to all Janelians. Most interest groups are recorded and can be accessed through Panopto internally, while some of them are publicly available on our YouTube channel.

We are looking forward to working with you!

Organization / Structure of SciComp Software

The director of SciComp Software is Stephan Preibisch and it consists of three teams: Software Engineering headed by Konrad Rokicki, Software Solutions, headed by Stuart Berg; and Computational Methods headed by Stephan Preibisch.

Each team conducts its own internal meetings. The entire group attends SciComp Software team meetings, during which the science discussions are open to interested parties.

SciComp organizes the Scientific Computing Associate (SCA) program that embeds SCA's in SciComp and the lab or team they work with. The Scientific Computing Interest Groups are run by SciComp engineers and SCA's. The Open Science Software Initiative is a collaboration between C&T and SciComp.

janelia7_blocks-janelia7_block_right_hand_rail | block

Projects & Tools

Find neuron matches across modalities

A cloud-based collaborative annotation system for terabyte-scale sparse volume annotation

 VVD Viewer
Volumetric renderer for 3D/4D microscopy data

 EASI-FISH pipeline
Portable pipeline for end-to-end analysis of spatial transcriptomics data

Web services for image transformation

Precise, interactive, fast, and scalable FISH spot detection

Efficient alignment of multi-tile and multi-angle image datasets

See also this curated list of Janelia software that is actively maintained either by Scientific Computing or individual labs.


Scientific Computing Associates Program

Looking for a wealth of challenging assignments that will satisfy your thirst for cutting-edge science, leverage and build on your coding skills, and launch your career in Computational Science? 

You may find a perfect fit in Janelia’s new Scientific Computing Associates program.

Learn More