nimbusimage

Plugin nimbusimage from marketplace NimbusImage in arjunrajlaboratory/NimbusImage. Commands read from the repo's manifest — 2 days ago.

Skills (7)

• analyze

  Compute properties, export data, manage connections, and share NimbusImage datasets using the nimbusimage Python API. Use this skill when the user wants to compute annotation measurements, export data as JSON or CSV, create connections between annotations, share datasets with collaborators, or manag

• annotations

  Create, list, filter, update, and delete annotations on NimbusImage datasets using the nimbusimage Python API. Use this skill when the user wants to work with annotations — creating points or polygons, filtering by shape or tags, bulk operations, geometry conversion (shapely, numpy masks), or progra

• images

  Fetch image data from NimbusImage datasets as numpy arrays using the nimbusimage Python API. Use this skill when the user wants to retrieve image frames, composites, z-stacks, crops, or channel data from a NimbusImage dataset. Also use when you see ds.images in code, or the user mentions getting pix

• nimbusimage

  Connect to a NimbusImage server and work with scientific imaging datasets using the nimbusimage Python API. Use this skill whenever the user mentions NimbusImage, wants to connect to a Girder-based imaging server, list or open datasets, or asks about the nimbusimage package. Also use when you see `i

• sg-ingest

  Load a Spatial Genomics (GenePS / sganalysis) data export into NimbusImage, one dataset per ROI: DAPI + GFP images, cell polygons, Leiden clusters as tags and a numeric property, UMAP, cell area, the full cell x gene matrix as a spatial table, and the transcript list as a Transcripts overlay. Use wh

• workers

  Run Docker-based computational workers on NimbusImage datasets using the nimbusimage Python API. Use this skill when the user wants to run segmentation, spot detection, property computation, or any Docker worker on their imaging data. Also use when you see ds.annotations.compute or ds.properties.com

• xenium-ingest

  Load a 10x Xenium spatial-transcriptomics bundle into NimbusImage: the morphology and H&E images, cell segmentation polygons, a gene-expression marker panel, clustering, a computed UMAP, and cell types as tags. Use this skill when the user mentions Xenium, 10x spatial data, cells.zarr, cell_feature_

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