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