tryppy

Tryppy is an open-source Python package designed to simplify segmentation, feature extraction, and classification of microscopy data from Trypanosoma brucei.
It has been developed specifically for the TrypTag dataset. The performance on other microscopy datasets has not been evaluated and may vary.

How to install

We provided several options to make the functionality of tryppy available to you. You can choose to install the package via pip or github into your python environment. Alternatively you can choose to use our code via the provided Docker container. This is especially usefull for an easy to use proof of concept, when trying out new data.

From Pypi

pip install tryppy

Here you find the official pypi website.

From Github

pip install git+https://github.com/himmiE/tryppy.git

Using Docker Hub (recommended)

An official Docker image is available to run tryppy without installing Python or any dependencies locally. If you have Docker installed, you can pull the latest image with:

docker build -t tryppy:latest .

docker run tryppy:latest

This launches an interactive Python shell with tryppy preinstalled.

How to use

No matter which approach you choose, you may want to look at the config.json file. (describe where it is to be found) This file is to be edited by you whenever you want to change something about the workflow. It is probably a good idea to save changes in a new config file, in case you break something. You can also change the filename to have different versions. You will be able to choose the right config file later in your code.

The Config File

When you first run your code a basic config-file will be created for you. ...

option	description	example_input
left foo	right foo
left bar	right bar
left baz	right baz

The Data

Use In Code

import NAME_OF_PACKAGE

# define the path for your data.
# if you have a custom config.json file, it should go here.
data_path = directory_where_data_should_do

# if you are handling multiple tasks with this package or are experimenting
# with different setups, you can rename the config file and pass the filename
# (relative to your defined data_path).

obj_name = NAME_OF_PACKAGE(data_path)
# alt: 
# obj_name = NAME_OF_PACKAGE(data_path, config_filename = 'save_all_config.json')

obj_name.run()

License

TODO