What is the main purpose of the slurm-workflow-guide skill?

It provides a structured, step-by-step framework for processing multiplexed imaging data on High-Performance Computing (HPC) clusters using the SLURM workload manager and KINTSUGI.

Does this skill help with HiPerGator specific configurations?

Yes, it includes specific guidance for HiPerGator environments, including partition settings and account configurations in the slurm/config.sh file.

How do I verify my SLURM jobs before actual submission?

The skill recommends using the 'kintsugi slurm submit . --dry-run' command to verify cycles, tile grids, and wavelengths before committing cluster resources.

Can I use this skill for non-imaging data?

While specifically optimized for KINTSUGI imaging pipelines including correction and stitching, its structural logic helps with general SLURM job configuration and monitoring patterns.

KINTSUGI SLURM Workflow Guide

Name: KINTSUGI SLURM Workflow Guide
Author: smith6jt-cop

bysmith6jt-cop

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データサイエンスとML

Guides users through a comprehensive 10-step pipeline for processing multiplex imaging data on SLURM-managed HPC clusters.

This skill provides a structured framework for researchers and developers using the KINTSUGI platform on High-Performance Computing (HPC) clusters like HiPerGator. It automates the complex transition from raw microscopy data to finalized results by offering precise guidance on project initialization, metadata configuration (experiment.json and CHANNELNAMES.txt), and SLURM job submission. It is essential for users needing to perform large-scale illumination correction, stitching, deconvolution, and extended depth of focus (EDF) while ensuring rigorous quality control and resource efficiency.

主な機能

01HPC-specific optimization for HiPerGator cluster environments

02Automated guidance for experiment metadata and channel naming configuration

031 GitHub stars

04Quality control protocols for verifying illumination, stitching, and deconvolution

05Detailed CLI commands for SLURM job submission, dry-runs, and monitoring

06Step-by-step multiplex imaging workflow from raw data to processed results

ユースケース

01Troubleshooting and monitoring large-scale image processing jobs on remote clusters

02Automating batch processing of large microscopy datasets via SLURM scripts

03Initializing and configuring new multiplex imaging projects for HPC processing

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add smith6jt-cop/skills_registry slurm-workflow-guide

For use in Claude.ai and ChatGPT

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