birm / ImageLoader.py

Python utility that also does image loading. Used for large scale image loading where images are already available and all that is needed is to extract and store the metadata.

Data Loader

Python utility to extract metadata from OpenSlide images and post them to a RESTful interface

Installation:

• Tested on python 3.5.0.
• pip install -r requirements.txt

Make sure you have LD_LIBRARY_PATH set up

Usage:

python dataLoader.py -i <inputCSVFile> -o <RESTinterface> -a <API key>

Input.csv

This is the format of input.csv

Id, study_id, File
test1,default,/data/images/CMU-1.svs
test2,default,/data/images/CMU-2.svs

where

• Id is the case_id of the image
• study_id is the study_id
• File is the file location on disk.

Issues

ImportError: libopenjp2.so.7: cannot open shared object file.

Run

export LD_LIBRARY_PATH=/usr/local/lib to fix this.