Compared the new packages/nanovirdx skeleton with Factory, eval-service, and DiffSim’s gen4ve2e application.
Kept DiffSim sourced from the internal Artifactory channel and updated NanoVirDx to diffsim >=0.1.98,<0.2 on Python 3.12 for macOS ARM and Linux.
Implemented DomainRepresentationBatch.from_vxdata: it retrieves each domain representation, resolves its linked tissue, cell, Gleason, and structure-tensor maps, and downloads those S3 resources through the real vxData SDK.
Implemented DiffsimSimulator with lazy setup, CPU/CUDA/MPS selection, histology-domain loading compatible with current OME-Zarr domain representations, DWI b100/b1000 and T2 simulation, deterministic postprocessing, NIfTI output, and derived ADC output.
Ran the end-to-end adapter and simulator on histodomainrep/EZ01050/6E.1_4_17_175003/preprocessed/component_0/v2.0 on macOS Metal. A fast demo used 1,000 walkers and 128x histology downsampling and returned a valid BPMRIBatch.
Lessons Learned: Pitfalls
Artifactory diffsim 0.1.98 predates the gen4ve2e branch’s newer domain_from_histo API. A downstream Git dependency is not appropriate; the small missing adapter can be implemented against the released Domain API.
virdx_ome.ZarrImage.resolution for current histology domain representations is in micrometers per pixel. DiffSim domain voxel sizes are SI meters, so the adapter must multiply by 1e-6.
Current v2.0 domain representations use the fine28 taxonomy plus graded IDs 128-139, while the reference app’s old mapping only covers 13 labels. A current mapping is required before simulation.
PyTorch MPS does not implement adaptive_max_pool3d; foreground-mask pooling must run on CPU and move back to the selected device.
Lessons Learned: Improvements
DiffSim should publish its current histology-domain adapter and a documented tissue-taxonomy mapping so downstream inference code does not duplicate scientific policy.
The knowledge base needs a DiffSim inference SOP that records supported package versions, OME resolution units, current tissue label IDs, standard sequence settings, and a small smoke-test configuration.
NanoVirDx needs explicit package targets/tests once its skeleton allows additional project files; the current package has no project.json or test files.
