Roimarker

Annotates region of interest (ROI) using matplotlib and Python.

• Draw rectangular ROIs with your mouse
• Quickly change to the next image by pressing N
• Adjust brightness/contrast with keys Z,X,C,V
• Undo with Ctrl+Z

Installing

pip install roimarker

Usage

A) Standalone tool

python -m roimarker DIRECTORY

Here, replace DIRECTORY with the folder containing all the image files to be annotated.

When finished, a markings.json file is created to the current working directory with the following structure:

{fn1: [ROI_1, ROI_2, ROI_3, ..], fn2: [ROI_1, ...], ...}

where
	ROI_i = [x,y,w,h]

B) In your programs

import matplotlib.pyplot as plt
from roimarker import Marker

# Create matplotlib figure and ax
fig, ax = plt.subplots()

# List of images to annotate
image_fns = ['image1.tif', 'image2.tif', 'image3.tif']

marker = Marker(fig, ax, image_fns, 'markings.json')
marker.run()