imageJ-ROIs

Scripts to convert ROIs to csvs, csvs to shapefiles using JAVA and Python

Dependencies that need to be installed are geopandas, shapely.geometry, Polygon, pandas, ast, argparse, os

To create a shapefile:

A) To create a shapefile

1. Open image and ROI manager in Imaje-J/FIJI

2. Open File->New Script and switch the Language to JavaScript

3. Copy paste "Coordinate_extractor_IMAGEJ_ROI_V2 code into the editor (or open file)

4. Change the output destination and name on line 16

   output_file = new FileWriter("C:/Users.../roi_coordinates.csv");

5. Open command terminal and switch directory to location of "both.py"

6. In command terminal type

   C:\Users\nicor> cd 'path to directory with both.py'

7. You should now see the new directory

8. Type

   python both.py 'path to .csv file created in javascript above'

This will create a clean csv with the ROI coordinates and a shapefile in the same location as input file

To create a SVG

Need to download and move jfreesvg (https://www.jfree.org/jfreesvg/) into Image-J/FIJI plugin folder

1. Open image and ROI manager in Image-J/FIGI

2. Opel File-> New Script and switch the language to python

3. Copy paste the svggenerator code or open file

4. Switch output to desired destination and name on line 34

   path = "C:/Users/nicor/Downloads/testsvg3.svg"