bioimageflow-sairpico-tools 0.1.6

SAIRPICO command-line tool wrappers for BioImageFlow

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.

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, used by HotspotDetection.

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, 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.