bioimageflow-sairpico-tools

BioImageFlow wrappers for the SAIRPICO command-line tools from bioimageit/PyFlow/Tools/Sairpico.

Tools

• GaussianPSF: wraps simggaussian3dpsf.
• GibsonLanniPSF: wraps simggibsonlannipsf.
• RichardsonLucyDeconvolution: wraps simgrichardsonlucy2d, simgrichardsonlucy2dslice, and simgrichardsonlucy3d.
• WienerDeconvolution: wraps simgwiener2d, simgwiener2dslice, and simgwiener3d.
• SpitfireDeconvolution: wraps simgspitfiredeconv2d, simgspitfiredeconv2dslice, and simgspitfiredeconv3d.
• MedianDenoising: wraps simgmedian2d, simgmedian3d, and simgmedian4d.
• CImgDenoising: wraps denoise.
• HotspotDetection: wraps hotSpotDetection.
• HotspotToSpots: converts hotspot images to spot coordinate tables.

The SAIRPICO deconvolution CLIs expose a -lambda option. Because lambda is a reserved Python keyword, BioImageFlow exposes this parameter as regularization_lambda in Python and schemas while still passing -lambda to the underlying CLIs.

Mode values are validated against explicit executable mappings before a subprocess starts. Numeric and boolean parameters are likewise validated for direct process_row() calls, not only through generated workflow schemas. All image-output defaults use fixed .tif templates because their ImageSpec declarations promise TIFF output.

Environments

The package declares three EnvironmentSpec instances:

• simglib: bioimageit::simglib==0.1.2, used by PSF, deconvolution, and median denoising tools.
• cimgdenoising: bioimageit::cimgdenoising==1.0.0, used by CImgDenoising.
• hotspot: bioimageit::hotspot==1.0.0 plus pinned PyPI NumPy, SciPy, imageio, and tifffile dependencies, used by HotspotDetection and HotspotToSpots. Hotspot build 2 declares its current libtiff ABI through the conda package metadata on every supported platform.

The original SAIRPICO inventory listed platform selectors for these packages:

• simglib: osx-64, win-64, linux-64.
• cimgdenoising: osx-64, win-64.
• hotspot: osx-64, osx-arm64, win-64, linux-64.

These are conda-backed command wrappers. Unit tests validate schemas, argument validation, command construction, diagnostic environment/version reports, and hotspot table conversion without requiring the real binaries. The environment/version checks are package diagnostics, not public BioImageFlow workflow tools. Synthetic CLI execution is limited to subprocess monkeypatching because the SAIRPICO binaries are not Python library calls and may not be available on every platform.