image_processing

This reference covers accessing raw pixel data, image rendering, and creating new images in OMERO.

Skills
Scientific
1

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/image-processing && curl -fsSL https://doutorai.pt/data/lib/skills__image-processing.md -o .claude/skills/image-processing/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# Image Processing & Rendering

This reference covers accessing raw pixel data, image rendering, and creating new images in OMERO.

## Accessing Raw Pixel Data

### Get Single Plane

```python
# Get image
image = conn.getObject("Image", image_id)

# Get dimensions
size_z = image.getSizeZ()
size_c = image.getSizeC()
size_t = image.getSizeT()

# Get pixels object
pixels = image.getPrimaryPixels()

# Get single plane (returns NumPy array)
z, c, t = 0, 0, 0  # First Z-section, channel, and timepoint
plane = pixels.getPlane(z, c, t)

print(f"Shape: {plane.shape}")
print(f"Data type: {plane.dtype.na

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