crop-export-single-cell-crops

crop-export-single-cell-crops exports per-cell crop packages from a completed segmentation result.

It is the step that turns a finished segmentation result into one crop per cell.

Purpose

Use this skill when you want:

  • masked or unmasked single-cell crops

  • per-cell image stacks that can be reviewed directly

  • per-cell image inputs for deep-feature analysis

Main Outcome

After this skill finishes, the segmentation result is no longer only a set of masks and tables.

You also have one crop package per segmented cell, with image stacks, masks, and a manifest that links each crop back to its original object.

Inputs

This skill reads:

  • a segmentation workflow root from cp-extract-segmentation-artifacts

  • a crop mode such as masked or unmasked

  • crop-export settings from the project config or explicit user options

  • an optional output directory

Outputs

  • image_stacks/*.tiff Multi-channel per-cell crops.

  • cell_masks/*.tiff Whole-cell masks for each crop.

  • nuclei_masks/*.tiff Nucleus masks for each crop.

  • single_cell_manifest.csv The manifest that ties all crop files back to the original segmented objects.

  • pipeline_skill_manifest.json The run record for this skill invocation.

Agent Demo

This page is based on a real local OpenClaw inspection of a completed crop-export result:

  • session id: crop-inspect-v2

  • recorded on 2026-05-06

  • model: vibe/gpt-5-mini

Request

I already have a completed demo segmentation result and exported masked single-cell crops from it. Please inspect the crop result under demo/workspace/outputs/agent_demo_crops_check_v2 and tell me what per-cell outputs are available there for review or deep-feature analysis.

Structured Trace

user_input:
I already have a completed demo segmentation result and exported masked single-cell crops from it. Please inspect the crop result under demo/workspace/outputs/agent_demo_crops_check_v2 and tell me what per-cell outputs are available there for review or deep-feature analysis.

recorded_turn:
- the saved OpenClaw turn answered this request directly
- the reply reported the crop-export folder structure
- the reply summarized the number of cropped cells in the manifest
- the reply explained the purpose of image stacks, cell masks, nuclei masks, and the manifest

final_answer_snapshot:
The completed crop export contains 4 masked single-cell examples, each with an image stack, a cell mask, a nucleus mask, and one manifest row.

Observed Result

The inspected completed crop export under agent_demo_crops_check_v2 contained:

  • masked/image_stacks/

  • masked/cell_masks/

  • masked/nuclei_masks/

  • masked/single_cell_manifest.csv

The manifest showed:

  • 4 cropped cells total

  • plate BR00000001

  • wells A01 and A02

  • site 1

Recorded Reply

I inspected the completed masked crop export under:

- `demo/workspace/outputs/agent_demo_crops_check_v2`

## What per-cell outputs are available there

This export contains a **masked single-cell crop set** produced from the completed demo segmentation result.

### Main output folders
Under:

- `demo/workspace/outputs/agent_demo_crops_check_v2/masked/`

you have:

- `image_stacks/`
- `cell_masks/`
- `nuclei_masks/`
- `single_cell_manifest.csv`

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