BioImageFlow SAIRPICO Tools¶
bioimageflow-sairpico-tools owns BioImageFlow wrappers for the SAIRPICO
command-line programs. The package exposes point-spread-function
generation, deconvolution, denoising, and hotspot detection tools while keeping
the original binaries in conda-backed EnvironmentSpec definitions.
The public tools are:
GaussianPSF: generate a 3D Gaussian PSF with
simggaussian3dpsf.GibsonLanniPSF: generate a 3D Gibson-Lanni PSF with
simggibsonlannipsf.RichardsonLucyDeconvolution: run 2D, 2D-slice, or 3D Richardson-Lucy deconvolution.
WienerDeconvolution: run 2D, 2D-slice, or 3D Wiener deconvolution.
SpitfireDeconvolution: run 2D, 2D-slice, or 3D SPITFIR(e) deconvolution.
MedianDenoising: run 2D, 3D, or 4D median filtering.
CImgDenoising: run the CImg
denoisecommand.HotspotDetection: run
hotSpotDetectionfor sparse hotspot detection.HotspotToSpots: convert hotspot images into spot tables.
The package declares three environments:
simglib:bioimageit::simglib==0.1.2fromconda-forgeandbioimageit; used by PSF, deconvolution, and median-denoising tools.cimgdenoising:bioimageit::cimgdenoising==1.0.0fromconda-forgeandbioimageit; used byCImgDenoising.hotspot:bioimageit::hotspot==1.0.0fromconda-forgeandbioimageit; used byHotspotDetection.
Inputs are image files, with public image wrappers declaring png, tif, and
tiff formats. The underlying SAIRPICO binaries are external
processes, so failures are usually surfaced as missing binaries, missing PSF
files for 3D deconvolution, unsupported file layouts, or non-zero subprocess
exit codes.
Environment availability and version reporting are covered by package diagnostics and tests instead of being exposed as public workflow tools. They do not produce image-analysis outputs and should not appear in analyst-facing workflow builders.
Workflow use:
Use the SAIRPICO deconvolution workflow in the main workflow catalog for PSF generation, denoising, deconvolution, and metrics.