medical imaging security · radiation oncology
I investigate security-relevant edge cases and data-integrity defects in medical imaging and scientific software, contribute focused upstream fixes, and maintain open-source binary inspection, privacy, and research tools for Apple Silicon (ARM64). My work emphasizes defensive DICOM/NIfTI parsing, archive extraction containment, filesystem access controls, safe HTML output, integrity verification, and enforcement of caller-specified safeguards.
I develop and maintain AIRS, EntitlementDiff, DICOM Anonymizer, and SidecarCompare for static binary inspection, entitlement auditing, imaging-data privacy, and reproducible metadata analysis. My clinical work in radiation oncology and research in MR imaging and radiomics inform this engineering work.
74 authored pull requests merged across 45 external repositories. The total spans security hardening, scientific data integrity, imaging workflows, platform support, and test improvements.
| Area | Merged contributions |
|---|---|
| Imaging parser hardening | NiBabel #1568 and NIFTI-Reader-JS #58: reject undersized NIfTI extension lengths before payload reads. highdicom #471: reject undefined encapsulated pixel-fragment lengths before payload reads. |
| Archive extraction containment | Nilearn #6654: check path components so a sibling directory sharing a name prefix is not accepted as an extraction destination. |
| Filesystem access controls | deid #304: default newly created pixel-cleaner output directories to owner-only permissions. fsspec #2358: preserve caller-selected SFTP directory modes when creating parents. |
| S3 request integrity | s3fs #1067: forward caller-supplied delete options, including expected bucket owner and MFA parameters. s3fs #1068: preserve exclusive-create conditions, requested ACLs, and metadata for zero-byte writes. |
| HTML output encoding | dicom-validator #301: escape filenames in validation-report headings so filename markup is rendered as text. |
| Temporary executable isolation | RSNA Anonymizer #41: place the compiled documentation helper in a private temporary directory for each process, avoiding reuse of a fixed-name executable. |
| Shell argument integrity | BIDScoin #302: quote image, output, and mask paths in local SynthStrip commands. |
| Supply chain reproducibility | dcm2niix #1046: pin the optional Cloudflare zlib dependency to a fixed source commit. |
| Archive checksum enforcement | PyMedPhys #2394: keep TRF archive checksum checks active under Python -O, preserving incoming logfiles when archived copies fail verification. |
I maintain the following MIT-licensed open-source projects, with a focus on explicit analysis scope, reproducible results, and preserving source data.
| Application | Security & research focus | Explore |
|---|---|---|
| AIRS | Native macOS workspace for bounded ARM64 Mach-O unwind analysis and app-entitlement comparisons. Reads inspected binaries as data, with analysis coverage and unresolved results made explicit. | Download the beta |
| EntitlementDiff | Review changes in declared macOS app entitlements between builds, with explicit architecture selection, exact typed values, and saved comparisons colleagues can reopen. Inspects the selected main executable without launching the app. | Download the macOS app |
| DICOM Anonymizer | Local DICOM metadata pseudonymization for MR, CT, and RTSTRUCT batches. Consistently remaps patient-specific UIDs and references, audits staged outputs, and preserves source files. | Download the beta |
| SidecarCompare | Review MRI acquisition-metadata changes using exact decimal comparisons, typed values, and documented units. Preserves both source sidecars and supports local snapshots and reports through a native SwiftUI app and shared CLI core. | Build the macOS app · Use the CLI |
My related research tooling includes Prism Native MCP, which connects original observations to native GraphPad Prism tables, descriptive analyses, editable graphs, and layouts.
| Area | Merged contributions |
|---|---|
| Array validation safeguards | PyTables #1387, #1388, and #1389: preserve coordinate views and read-only indices, reject non-integer Atom dimensions, and validate selectors before conversion, reads, or writes. |
| Atomic download publication | BrainStat #385: stage downloads and replace the destination only after a successful copy, preserving an existing file when copying fails. |
| File overwrite prevention | fonttools #4342: stage archives beside the destination before replacement, preserving unrelated sibling ZIPs and existing output if archive creation fails. svglib #518: parse compressed SVG input directly, preserving sibling SVG files and relative-image resolution. |
| Validation state isolation | dicom-validator #303: restore the caller's pydicom reading-validation mode after file validation, including exceptional exits. |
| Metadata path integrity | ANTsPy #931: keep JSON sidecars adjacent to NumPy images by replacing only the terminal .npy suffix, with migration guidance for legacy metadata paths. |
| Analysis evidence integrity | REA #5765: preserve mixed-slice Mach-O signature observations and partial evidence. REA #5763: align session-discovery capabilities with supported target operations. |
| SBOM parser resilience | CycloneDX Core Java #957: recognize JSON/XML software bills of materials with leading whitespace. |
| Security notification fidelity | Dependency-Track #7704: expose the latest project status in notification subjects. |
| Area | Merged contributions |
|---|---|
| Failure handling resilience | Pillow #10271: handle zero-width images in ImageOps.cover() without division by zero. ANTsPy #924: reject failed HTTP responses before caching test data. pyplastimatch #15: propagate conversion and resampling failures to callers. |
| macOS architecture compatibility | ITK #6947: use the requested macOS target architecture for FFTW SIMD defaults. dcm2niix #1043: support linking from source paths containing spaces. Additional merged SDK, architecture, and toolchain fixes are recorded in the contribution index. |
| Shell path safety | ITK-SNAP #280: preserve spaced application paths in the macOS launcher. FastSurfer #950: quote FreeSurfer stub destinations during helper generation. |
| Buffering policy enforcement | fsspec #2359: preserve explicitly requested zero buffering for immediate and deferred SFTP opens. |
| ARM64 integration testing | Add JPEG and JPEG 2000 plugin coverage, including pydicom integration, in pylibjpeg-libjpeg #91 and pylibjpeg-openjpeg #129. Add CI coverage to zarrs #490, zarrs-python #199, connected-components-3d #153, fastremap #60, and FabIO #675. |
| Test suite reliability | Nilearn #6664: stabilize plotting-test parameter order for parallel collection. xarray #11780: guard a DataFrame-conversion test with its optional PyArrow dependency. silx #4745: support Qt 6.12 drag-event constructors while retaining compatibility with older Qt versions. |
The full contribution index also preserves documentation, issue reports, additional proposals, and fork work with links to the original records.
I combine source review, static binary analysis, and focused regression testing to trace failures to specific parsing, filesystem, process, or data-handling boundaries. I favor small, reviewable patches with explicit supported scope and reproducible evidence. My maintained DICOM Anonymizer includes a documented private security-reporting process and guidance for synthetic reproductions.
For imaging and radiomics, numerical values, units, acquisition metadata, and source lineage matter as much as successful execution. My tools preserve inputs, expose failures and unresolved results, and distinguish declared configuration from observed behavior.
I welcome collaboration on medical imaging security, radiomics infrastructure, defensive binary analysis, and native Apple Silicon applications.