CZI EOSS Grantees

Public

Projects funded by the Chan Zuckerberg Initiative's Essential Open Source Software for Science (EOSS) program. CZI EOSS supports software projects that are essential to biomedical research and the broader scientific community. The program recognizes that much of modern science depends on open source software, and invests in the maintenance, growth, and sustainability of these critical tools. This portfolio spans a wide range of scientific domains: - Bioinformatics & genomics (GATK, samtools, Nextflow, Snakemake, Bioconductor) - Neuroimaging (fMRIPrep, FreeSurfer, MNE-Python, Nilearn) - Microscopy & imaging (napari, ImageJ/Fiji, QuPath, Bio-Formats) - Single-cell analysis (Scanpy, Seurat, scvi-tools, AnnData) - Core scientific computing (NumPy, SciPy, pandas, Matplotlib, scikit-learn) - Statistical modeling (Stan, PyMC, ArviZ) - Data infrastructure (JupyterLab, Dask, conda-forge, Zarr) Together these ~200 projects form the backbone of open source scientific software.

Created 4/9/2026 - Last updated 7/28/2026

257

Projects

1.8M commits

114.9K

Recognition

96.6K citing papers · 51 canonical works

1.8M

Reach

29.6K external users · 2592.7M downloads

Repositories at risk

29% of 250 evaluated · 177 healthy · 7 unverified

226

Without canonical credit

of 257 · 12% have detected canonical

643 unwrapped

Metadata coverage

repo → publication funnel

Projects in this portfolio257100%

with any publication linkage8633%

with canonical paper detected3112%

distinct canonical works3514%

canonical

mentions

145

paper

Of 257 projects in this portfolio, 171 (67%) have no detected publication linkage of any kind. These gaps are part of the story — software metadata in the wild is often missing.

Top recognized work

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Most-cited publications representing software in this portfolio — the academic credit going to these projects. Items marked "detection gap" are likely portfolio software whose canonical link our pipeline failed to record.

1.
Matplotlib: A 2D Graphics Environment
37,869 citations · 10.1109/mcse.2007.55
2.
Array programming with NumPy
detection gap
20,849 citations · should be canonical for numpy · 10.1038/s41586-020-2649-2
3.
<scp>UCSF ChimeraX</scp>: Structure visualization for researchers, educators, and developers
9,675 citations · 10.1002/pro.3943
4.
3D Slicer as an image computing platform for the Quantitative Imaging Network
8,526 citations · 10.1016/j.mri.2012.05.001
5.
QuPath: Open source software for digital pathology image analysis
detection gap
8,198 citations · should be canonical for qupath · 10.1038/s41598-017-17204-5
6.
scikit-image: image processing in Python
6,689 citations · 10.7717/peerj.453
7.
PsychoPy2: Experiments in behavior made easy
5,220 citations · 10.3758/s13428-018-01193-y
8.
Nextflow enables reproducible computational workflows
4,111 citations · 10.1038/nbt.3820
9.
MEG and EEG data analysis with MNE-Python
3,809 citations · 10.3389/fnins.2013.00267
10.
ilastik: interactive machine learning for (bio)image analysis
3,507 citations · 10.1038/s41592-019-0582-9

External foundational dependencies

Upstream tools the portfolio depends on whose home repos are not in this portfolio. The citation counts here belong to the cited work — they show what these projects are built on, not what this portfolio is cited for.

1.
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
26,786 citations · used by 1 repo · 10.1093/molbev/msu300
2.
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
26,638 citations · used by 1 repo · 10.1089/cmb.2012.0021
3.
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
23,068 citations · used by 1 repo · 10.1038/s41587-019-0209-9
4.
Model-based Analysis of ChIP-Seq (MACS)
19,576 citations · used by 1 repo · 10.1186/gb-2008-9-9-r137
5.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
18,743 citations · used by 1 repo · 10.1093/sysbio/syq010
6.
ModelFinder: fast model selection for accurate phylogenetic estimates
17,996 citations · used by 1 repo · 10.1038/nmeth.4285
7.
Minimap2: pairwise alignment for nucleotide sequences
16,048 citations · used by 1 repo · 10.1093/bioinformatics/bty191
8.
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
15,730 citations · used by 1 repo · 10.1093/molbev/msaa015
9.
Data Structures for Statistical Computing in Python
10,787 citations · used by 1 repo · 10.25080/majora-92bf1922-00a
10.
UFBoot2: Improving the Ultrafast Bootstrap Approximation
10,600 citations · used by 1 repo · 10.1093/molbev/msx281

People & places

Bridge contributors

2,986

people contribute to 2+ projects in this portfolio · 28% of all contributors

Top citing institutions

Centre National de la Recherche Scientifique(FR)5,229
Harvard University(US)2,335
University of Oxford(GB)2,264
University of Cambridge(GB)1,983
Stanford University(US)1,867

Explore Full Interactive Graph

Impact

114.9K

Total Citations

96.6K

Citing Papers

204

Linked Publications

83.5K

Software Dependents

373.5K

Citing Authors

23.3K

Citing Institutions

Biochemistry, Genetics...

Top Citing Field

	Portfolio	Citing
Domains	4	4
Fields	18	26
Subfields	60	246
Topics	155	3645

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Dependencies

55.6K

Total Dependencies

Ecosystems

455

Research SW Links

575

Hidden Found

Ecosystem	Packages
pypi	19298
npm	15883
actions	8190
conda	7301

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Community

163 items at risk — review sustainability

11.9K

Total People

Retention Rate

52.4%

Intl. Collaboration

16 pubs · 147 repos

At Risk

	Pubs	Repos
Core	148	...
Active	45	10750
Bus Factor	-	1

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MCP Ecosystem

643 entities have no MCP wrapper — potential funding gaps

643

Unwrapped Entities

661

Portfolio Entities

130

Wrapping Servers

97%

Gap Rate

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