omero-integration

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

1.49x

Quality

62%

Does it follow best practices?

Impact

88%

1.49x

Average score across 3 eval scenarios

Securityby

Advisory

Suggest reviewing before use

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/omero-integration/SKILL.md

Evaluation results

82%

Microscopy Image Processing Pipeline

Image processing pipeline with physical dimensions

Criteria

Without context

With context

Context manager connection

100%

Default port 4064

100%

Env var credentials

100%

getPrimaryPixels plane access

100%

60%

0-indexed channel pixel access

100%

Generator for image creation

100%

createImageFromNumpySeq

100%

Physical size with LengthI

100%

50%

saveObject for pixel update

62%

100%

Error handling

100%

uv pip install

94%

38%

Automated Cell Region Analysis and Results Storage

ROI creation, intensity measurement, and OMERO tables

Criteria

Without context

With context

omero.model.RoiI creation

100%

rdouble/rint/rstring for shape props

100%

rgba_to_int for colors

100%

getShapeStatsRestricted

100%

getRoiService

100%

OMERO table initialization

100%

Correct column types

100%

StringColumn with max_length

table.close() called

100%

FileAnnotationI table linking

100%

BlitzGateway context manager

100%

88%

46%

Multi-Group Microscopy Metadata Audit Tool

Structured metadata annotations and cross-group data access

Criteria

Without context

With context

Cross-group query setOmeroGroup

100%

MapAnnotationWrapper usage

100%

NSCLIENTMAPANNOTATION namespace

Custom namespace reverse domain

25%

100%

createFileAnnfromLocalFile

100%

CSV MIME type

75%

100%

linkAnnotation

100%

Env var credentials

100%

BlitzGateway context manager

100%

metadata_design.md content

85%

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Microscopy Image Processing Pipeline Automated Cell Region Analysis and Results Storage Multi-Group Microscopy Metadata Audit Tool

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