sciagent-skill-creator
Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends…
NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration policy, and strict image integrity requirements.
$ npx -y skills add jaechang-hits/SciAgent-Skills --skill nejm-figure-guide --agent claude-codeHow it fires
How this skill gets triggered: by you, by Claude, or both.
/nejm-figure-guideContext preview
The summary Claude sees to decide when to auto-load this skill.
NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration policy, and strict image integrity requirements.
name: nejm-figure-guide description: "NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration policy, and strict image integrity requirements." license: CC-BY-4.0 compatibility: Python 3.10+, Pillow, Matplotlib metadata: authors: HITS version: "1.0"
This guide provides the complete specifications for preparing figures for submission to the **New England Journal of Medicine (NEJM)**. A unique feature of NEJM is that **medical illustrations are created by NEJM's in-house illustrators** working directly with authors — authors should NOT submit finished medical illustrations due to copyright considerations.
**Official reference**: https://www.nejm.org/author-center/new-manuscripts
---
| Image Type | Minimum Resolution | Notes | |---|---|---| | Black-and-white line art | **1,200 DPI** | Highest requirement | | Photographic / halftone images | **300 DPI** | Standard for photographs | | Peer review stage | Lower resolution acceptable | High-res required for final publication |
from PIL import Image
def check_nejm_resolution(image_path, image_type='photo', stage='final'):
"""Check if image meets NEJM resolution requirements.
Args:
image_type: 'lineart' (1200 DPI) or 'photo' (300 DPI)
stage: 'review' (lower OK) or 'final' (strict requirements)
"""
min_dpi = {'lineart': 1200, 'photo': 300}
required = min_dpi.get(image_type, 300)
if stage == 'review':
print("NOTE: Lower resolution acceptable for peer review")
required = 150 # relaxed for review
img = Image.open(image_path)
dpi = img.info.get('dpi', (72, 72))
print(f"Stage: {stage} | Type: {image_type}")
print(f"Required: {required} DPI | Actual: {dpi[0]} DPI")
passed = dpi[0] >= required
print("PASS" if passed else "FAIL")
return passed---
| Figure Type | Preferred Format | Notes | |---|---|---| | Data visualizations (graphs, plots, diagrams) | **AI, EPS, SVG** | Editable vector files preferred | | Photographic images | **TIFF** | High-resolution raster | | Medical illustrations | **Do NOT submit** | NEJM illustrators create these |
**IMPORTANT**: NEJM's in-house medical illustrators will work directly with authors to create medical illustrations. Authors should NOT submit finished illustrations due to copyright considerations. The journal retains copyright on illustrations created by their team.
---
NEJM does not publish detailed size specifications in their public guidelines. General best practices:
---
---
| Element | Specification | |---|---| | Preferred style | **Sans-serif** | | Historical font | Univers (NEJM house font) | | Alternatives | Helvetica, Arial |
import matplotlib.pyplot as plt
def set_nejm_fonts():
"""Configure Matplotlib for NEJM figure fonts."""
plt.rcParams.update({
'font.family': 'sans-serif',
'font.sans-serif': ['Univers', 'Helvetica', 'Arial'],
'font.size': 8,
'axes.labelsize': 8,
'axes.titlesize': 8,
'xtick.labelsize': 7,
'ytick.labelsize': 7,
'legend.fontsize': 7,
})---
def check_clinical_image_text(title, legend):
"""Validate text limits for NEJM Images in Clinical Medicine."""
title_words = len(title.split())
legend_words = len(legend.split())
issues = []
if title_words > 8:
issues.append(f"Title has {title_words} words (max 8)")
if legend_words > 150:
issues.append(f"Legend has {legend_words} words (max 150)")
if issues:
for issue in issues:
print(f"ISSUE: {issue}")
else:
print(f"PASS: Title ({title_words} words), Legend ({legend_words} words)")
return len(issues) == 0---
---
from PIL import Image
import os
def validate_nejm_figure(image_path, image_type='photo', stage='final'):
"""Full validation of a figure against NEJM requirements."""
img = Image.open(image_path)
issues = []
# 1. Resolution check
min_dpi = {'lineart': 1200, 'photo': 300}
required = min_dpi.get(image_type, 300)
if stage == 'review':
required = 150
dpi = img.info.get('dpi', (72, 72))
if dpi[0] < required:
issues.append(f"Resolution {dpi[0]} DPI below {required} DPI for {image_type} ({stage})")
# 2. Color mode
if img.mode not in ('RGB', 'RGBA', 'L'):
issues.append(f"Color mode {img.mode} may not be ideal; use RGB or Grayscale")
# 3. Format checkTurn your AI coding agent into a life sciences expert — 199 bioinformatics skills for Claude Code covering RNA-seq, single-cell analysis, genomics, proteomics, drug discovery, and more. Boosted BixBench from 65% to 92%. Open source.
Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends…
Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP…
Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent…
Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for…
Python statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference,…
DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm…