Python viewer brings together deep learning community and lab scientists

Datasets in science are getting big and unruly. Thankfully, there are people like Carsen Stringer to wrangle them into shape.

A few years ago, she started looking for a way to process terabytes of brain images collected across HHMI’s Janelia Research Campus, where she’s a group leader. Stringer wanted a tool to automatically label different types of neurons. But out-of-the-box products struggled; they had to be retrained for each kind of cell being studied.

So she created Cellpose. Coded in Python, this deep learning-based algorithm segments images into cells using a technique called flow representation.

Cultured neuroblastoma cells segmented by the napari plugin Cellpose. Credit: Carsen Stringer.

Then Stringer hit a roadblock…


Introducing Aspen, an Open-Source Tool To Help Departments of Public Health Track and Slow the Spread of COVID-19 and Prepare for Future Crises

As COVID-19 quickly spread across California and the U.S. in the spring of 2020, our teams at the Chan Zuckerberg Initiative (CZI) and the Chan Zuckerberg Biohub (CZ Biohub) believed that two approaches had the potential to significantly impact the spread of the virus. The first was increased availability of testing to help identify cases and better understand its spread in real time. The second was genomic analysis of positive samples to determine how and where the virus was mutating.

To address the testing shortage, CZI and CZ Biohub, along with hundreds of volunteers from UC San Francisco, turned an…


The Carpentries is an organization dedicated to teaching researchers computational skills through a scalable and community-centered model. Since 2019, CZI and the Gordon and Betty Moore Foundation are supporting The Carpentries’ instructor training program and the development of CarpentriesLab — a centralized repository for high-quality, teaching materials contributed by the community. This post was authored by The Carpentries’ team.

“Teaching Carpentries workshops is a good way for me to learn more about best practices in computing, and to share that knowledge with other people in the scientific world. This makes me feel like I’m doing what science is supposed to…


A Conversation with Hannah Valantine and Cori Bargmann

Biomedical science, just like our healthcare system, is rife with structural disparities, inequities, and injustices that are especially experienced by Black, Latinx, and Indigenous people, and other communities of color. These inequities and lack of representation impede innovative and trustworthy science — good science must be guided by principles of diversity, equity, and inclusion (DEI).

We recognize we will not achieve our mission of supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century unless we actively work to dismantle racism and systemic barriers in the scientific…


As the old adage says, two heads are better than one.

Last year, as part of our Collaborative Pairs Pilot Projects RFA, we welcomed 30 pairs of researchers to our Neurodegeneration Challenge Network (NDCN). Collaborative Pairs is a unique grant program designed to catalyze new types of collaborations and encourage bold “out-of-the-box” ideas for tackling challenges related to the basic science of neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and ALS.

These pairs bring interdisciplinary and transformative approaches to studying these diseases, leveraging the power of collaboration to accelerate science. Many of these investigators are new to neurodegeneration research, and at…


Takeaways from user experience research on the new napari hub

We want to make it easier for biologists to analyze microscopy imaging data and to access emerging methods for bioimage analysis that leverage machine learning. To that end, for the past year, the CZI imaging tech team has partnered with the napari image viewer to enable high performance visualization and exploration of a broad range of imaging data. We’ve also conducted foundational user experience research studies to better understand the community we’re building for.

A video of the napari visualization interface, browsing and segmenting cells infected with SARS-CoV-2 virus from a high-throughput screen. Data from Recursion Pharmaceuticals.

Creating a hub for plugins

For our latest project, we are building a site that biologists can rely on to find quality reproducible bioimage analysis workflows that are compatible with napari…


How the Neurodegeneration Challenge Network creates connections to accelerate disease research

When the Neurodegeneration Challenge Network (NDCN) — one of CZI’s flagship science programs — launched a little more than two years ago, we began a deliberate experiment in science community building. We envisioned an interdisciplinary collaborative network that would bring new ideas and new people into the field of neurodegeneration, with the common goal of developing innovative strategies for the treatment and prevention of neurodegenerative diseases. It would try to shift the field from looking at neurodegenerative diseases separately to examining them collectively. …


What do business executives, stay-at-home moms, a PhD scientist, community organizer, computer scientist, and former professional basketball player all have in common?

These individuals are some of the inspiring leaders of patient-driven organizations fighting tirelessly for cures, treatments, and therapies to one of 7,000 known rare diseases.

As part of the Rare As One Project, we’re supporting 30 patient-led rare disease organizations that are working to develop and strengthen a collaborative research network in their disease area, convene their research community, and align around shared research priorities. …


Celebrating Learnings from the Rare As One Project and Launching a Second Funding Opportunity

Each February, the rare disease community comes together and celebrates Rare Disease Month to raise awareness about rare diseases, their impact on patients’ lives, and the urgent need to find treatments and cures. Rare Disease Month culminates in Rare Disease Day on the last day of February — the rarest day of the year.

This year, we’re reflecting on the progress our grantees in the Rare As One Network have made to accelerate research — despite facing significant challenges brought on by the COVID-19 pandemic — and our learnings along the way. …


Transforming bioinformatics into a guiding force in research

For a scientist destined to earn renown for her skill in creating biostatistical tools and extracting meaning from large datasets, Katherine Pollard’s initial impulses toward the study of math were somewhat conflicted: “I wasn’t sure I saw myself as a math major, until a professor convinced me to think about it,” she says of her first collegiate year.

By graduation, she had arrived at a happy medium between numbers and her interest in human physiology and evolution: a double major in mathematics and anthropology. …

Chan Zuckerberg Science Initiative

Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.

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