gin-moth 0.1.0

Memory-efficient On-the-fly Tiling of Histological images

MOTH

MOTH (Memory-efficient On-the-fly Tiling of Histological images using QuPath) is a Python library that extends the functionality of paquo.

The added functionalities are functions to support tiling in QuPath directly from Python. Now tiling can be done on-the-fly with moth and a Python developer no longer needs a Groovy script to generate tiles.

The documentation can be found under gin-moth.readthedocs.io.

Installation

moth can be installed via pip:

 user@computer:~$ pip install gin-moth

Install QuPath

To interact with QuPath, paquo (package that moth extends) requires a working QuPath installation.
To install QuPath follow the QuPath installation guide: Install QuPath.

QuPath can also be installed with a paquo helper script documented here.

If QuPath is not installed in the default directory, you need to configure QuPath for paquo via:

  user@computer:~$ export PAQUO_QUPATH_DIR=/path/to/QuPath

or via the configuration of paquo.

Install via Docker

To get a ready to use (python, moth and QuPath installed) Docker container, clone the repository and use the Dockerfile from github to create a new Docker image.
To use the Dockerfile follow the below steps for creating an image:

  user@computer:~$ docker build [-t tagname] .

now run the container using:

  user@computer:~$ docker run -it tagname bash

To mount files or data, explore the docker run documentation