Why is marker-based naming preferred over channel numbers?

Downstream analysis and QC tools like Kview_qc.py use specific search strategies that expect marker names (e.g., CD3.tif). Numeric names like CH1_edf.tif often cause pipeline breaks.

How does this skill handle missing metadata files?

It includes a get_channel_name fallback function that reverts to standard 'CH#' naming if CHANNELNAMES.txt is unavailable, ensuring the job completes successfully.

Which HPC environments is this skill compatible with?

It is optimized for HiperGator but applies to any SLURM-based cluster running the KINTSUGI image processing pipeline.

Does this skill address memory issues in SLURM jobs?

Yes, it provides guidance on matching EDF memory allocation to deconvolution requirements to prevent common OOM (Out of Memory) exit 137 errors.

KINTSUGI SLURM Channel Naming

Name: KINTSUGI SLURM Channel Naming
Author: smith6jt-cop

bysmith6jt-cop

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数据科学与机器学习

Standardizes SLURM job output naming by mapping channel numbers to biological marker names for the KINTSUGI pipeline.

This skill resolves critical naming discrepancies between SLURM batch jobs and Jupyter notebooks within the KINTSUGI image processing framework. By implementing canonical channel name loading from metadata files, it ensures that Extended Depth of Field (EDF) outputs are correctly named (e.g., 'CD3.tif' instead of 'CH1_edf.tif'). This alignment is essential for downstream compatibility with quality control scripts and visualization tools, preventing 'file not found' errors and ensuring robust data provenance on High-Performance Computing (HPC) clusters like HiperGator.

主要功能

01Synchronizes SLURM output naming with KINTSUGI notebook conventions

02Optimizes SLURM memory allocation for large-scale z-stack processing

03Configures Python sys.path for complex HPC directory structures

041 GitHub stars

05Provides automatic fallback to channel numbers when metadata is missing

06Implements canonical CHANNELNAMES.txt parsing via the Kio utility

使用场景

01Standardizing image file naming across large-scale multi-cycle experiments

02Fixing downstream _find_edf_file failures in Kview_qc scripts

03Automating KINTSUGI pipeline deployments on SLURM-managed HPC clusters

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add smith6jt-cop/skills_registry slurm-edf-channel-naming

For use in Claude.ai and ChatGPT

Download Skill