alterlab-omero
From the author
Manages microscopy image data on an OMERO server via the OMERO Python API (BlitzGateway) — access images, retrieve datasets, read pixel data, manage ROIs and annotations, and batch-process. Use when connecting to an OMERO server, pulling microscopy images or datasets, analyzing pixels, managing ROIs/annotations, or running high-content screening and microscopy workflows. Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-omero -a claude-code
Installs to .claude/skills/alterlab-omero/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
Want your agent to suggest skills while you type? See how to use skills from your IDE.
Safety checks on SKILL.md
No warnings.
Why 83
aiqbench computes the trust score from public signals. It is not a security audit, so read a skill before you install it.
Similar skills
Closest to this one by what they do and when they are used.
- omero-integrationK-Dense-AI/scientific-agent-skillsInspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use this skill for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.Media★ 54.5K
- alterlab-pyzoteroAlterLab-IEU/AlterLab-Academic-SkillsInteract with Zotero reference management libraries using the pyzotero Python client — retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero. Part of the AlterLab Academic Skills suite.Documents★ 78
- alterlab-generate-imageAlterLab-IEU/AlterLab-Academic-SkillsGenerates or edits raster images via AI models (FLUX.2, Gemini 3.1 Flash Image / "Nano Banana 2") through an OpenRouter API key. Use when the request is to generate or edit a photo, illustration, artwork, concept art, poster hero image, or presentation/slide visual asset — anything that is not a technical diagram, an infographic, or a data chart. For flowcharts, circuits, pathways, neural-net architectures, and technical/methodology diagrams use alterlab-scientific-schematics; for infographics that lay out statistics or timelines use alterlab-infographics; for plotting numeric data (scatter, bar, line) use alterlab-matplotlib instead. Part of the AlterLab Academic Skills suite.Media★ 78
- alterlab-pydicomAlterLab-IEU/AlterLab-Academic-SkillsReads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images, anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM to other formats, handling compressed DICOM, or processing medical imaging datasets for PACS systems, radiology workflows, and healthcare imaging applications. Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-biopythonAlterLab-IEU/AlterLab-Academic-SkillsManipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez — for quick one-off database lookups use gget, for unified multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.Data★ 78
- alterlab-anndataAlterLab-IEU/AlterLab-Academic-SkillsBuild, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.Writing★ 78
Ratings & reviews
—
no reviews
Tried this skill? Rate it to help others. Sign in
Discussion
Join the discussion. Sign in