FlowRegSuite/flowreg-agent-skills
Plugin Claude Code
FlowRegSuite Agent Skills: plan, execute and quality-control dense Flow-Registration motion correction for 2D, multi-session, axial z-drift and volumetric 3D microscopy data.
FlowRegSuite/flowreg-agent-skills
Instructions file CodexOpenCode
AGENTS.md instructions for FlowRegSuite/flowreg-agent-skills, covering what this repository is, hard rules, layout and before you finish.
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Reproduce or audit the published Flow-Registration benchmarks against pinned source revisions, covering the 512x512 synthetic clean/35 dB/30 dB conditions, one- and two-channel variants, the 6.2 Hz and 30.9 Hz MATLAB reproduction scripts, coordinate and sign conventions, and NoRMCorre comparison parameters. Use when a…
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Estimate and optionally correct spatially resolved axial z drift in a 2D microscopy recording relative to a reference volume, with verified axes, spacing, anchor, search-window, and patch settings. Use when an imaging plane moves through a known z stack. Do not use for native 3D-to-3D registration or ordinary in-plane…
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Inspect microscopy data and select the appropriate FlowRegSuite workflow, runtime, reference strategy, pilot, resource plan, and quality-control gates. Use before dense 2D correction, multi-recording common-reference alignment, reference-volume z-drift correction, or native volumetric 3D registration, especially when…
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Audit FlowRegSuite outputs and provenance after 2D, session, z-drift, or 3D workflows. Use to evaluate residual motion, displacement plausibility, valid regions, z-boundary behavior, channel consistency, output completeness, and reproducibility. Never declare successful correction solely from a completed process or…
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Plan, pilot, execute, and validate dense 2D Flow-Registration for one microscopy time series, including multichannel recordings, narrow regions of interest, rigid pre-alignment, and saved displacement fields. Use for x-y motion within a single 2D recording. Do not use for multi-recording common-reference alignment…
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Plan, pilot, execute, and validate native dense 3D registration with flowreg3D, including voxel spacing, memory checks, CPU or GPU selection, and three-component displacement fields. Use for moving volumes or time-resolved volumetric microscopy. Do not use for slice-wise 2D stack alignment or z drift of a single…
FlowRegSuite/flowreg-agent-skills
Skill Claude CodeCodex
Align multiple microscopy recordings into a common coordinate system using verified pyflowreg session stages: per-recording correction, between-recording reference alignment, and consensus valid masks. Use for longitudinal, multi-file, or multi-session studies requiring shared coordinates and resumable processing. Do…