pyimagej-fiji-bridge SKILL.md skillA
pyimagej-fiji-bridge from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pyimagej-fiji-bridge@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/cell-biology/pyimagej-fiji-bridge/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 24,908 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# PyImageJ — Python Bridge to ImageJ/Fiji ## Overview PyImageJ provides a Python interface to ImageJ2 and Fiji through PyJNIus and scyjava, embedding a full Java Virtual Machine inside a Python process. It enables bidirectional data exchange between NumPy arrays and ImageJ's ImagePlus/ImgLib2 data structures, so you can preprocess images in Python, pass them into Fiji plugins (Bio-Formats, TrackMate, Analyze Particles, Weka segmentation), and return results back to pandas DataFrames. The library supports headless operation for scripting and batch processing, as well as GUI mode for interactive Fiji sessions. ## When to Use - Running Fiji-specific plugins from Python: Bio-Formats multi-format I/O, TrackMate particle tracking, CLIJ2 GPU processing, or community Fiji update site plugins - Automating ImageJ macro pipelines headlessly without opening the Fiji GUI, e.g., batch processing an entire experiment overnight - Applying the ImageJ Ops framework (150+ image processing operations) with the full ImageJ type system - Converting between NumPy arrays (SciPy ecosystem) and ImageJ hyperstacks (TZCYX channel order) for round-trip processing …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pyimagej-fiji-bridge@sha256:f8580655612fabfdThe line at the top of this page pins the label git:20260428.81ea2d2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_lap2jafe66m2q5w2)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 24,908 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 25,040 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (24908 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_lap2jafe66m2q5w2 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pyimagej-fiji-bridge GET https://markdownregistry.com/api/v1/blob/f8580655612fabfdbead82fb27bafe31bfbf4ac20d7b0164deb9fe5435ea211a
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.