semvec/pypi-packages huggingface dataset:
DigiPathAI 0.1.5
Deep Learning toolbox for WSI (digital histopatology) analysis

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# DigiPathAI
A software application built on top of [openslide](https://openslide.org/) for viewing [whole slide images (WSI)](https://www.ncbi.nlm.nih.gov/pubmed/30307746) and performing pathological analysis 

### Citation
If you find this reference implementation useful in your research, please consider citing:
```
@article{khened2020generalized,
  title={A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis},
  author={Khened, Mahendra and Kori, Avinash and Rajkumar, Haran and Srinivasan, Balaji and Krishnamurthi, Ganapathy},
  journal={arXiv preprint arXiv:2001.00258},
  year={2020}
}
```
# Features
- Responsive WSI image viewer 
- State of the art cancer AI pipeline to segment and display the cancerous tissue regions

# Application Overview
<p align="center">
  <img src="imgs/demo.gif">
</p>

# Results
<p align="center">
  <img width="460" height="300" src="imgs/results_1.png">
</p>

# Online Demo
https://digipathai.tech/

# Installation
Running of the AI pipeline requires a GPU and several deep learning modules. However, you can run just the UI as well.

## Just the UI
### Requirements
- `openslide`
- `flask`

The following command will install only the dependencies listed above.
```
pip install DigiPathAI
```

## Entire AI pipeline
### Requirements
- `pytorch`
- `torchvision`
- `opencv-python`
- `imgaug`
- `matplotlib`
- `scikit-learn`
- `scikit-image`
- `tensorflow-gpu >=1.14,<2`
- `pydensecrf`
- `pandas`
- `wget`

The following command will install the dependencies mentioned
```
pip install "DigiPathAI[gpu]"
```

Both installation methods install the same package, just different dependencies. Even if you had installed using the earlier command, you can install the rest of the dependencies manually. 

# Usage 
## Local server
Traverse to the directory containing the openslide images and run the following command.
```
digipathai <host: localhost (default)> <port: 8080 (default)>
```

## Python API usage
The application also has an API which can be used within python to perform the segmentation. 
```
from DigiPathAI.Segmentation import getSegmentation

prediction = getSegmentation(img_path, 
			patch_size  = 256, 
			stride_size = 128,
			batch_size  = 32,
			quick       = True,
			tta_list    = None,
			crf         = False,
			save_path   = None,
			status      = None)
```

# Contact
- Avinash Kori (koriavinash1@gmail.com)
- Haran Rajkumar (haranrajkumar97@gmail.com)
md-toc-creator 1.4.1
Generates a table of contents for a markdown document in markdown.

# MD TOC
  A tool to create tables of contents from markdown files, in markdown
  format.

## Introduction

  md-toc-creator is a tool written in python that adheres to the old
  Unix philosophy of doing one thing and one thing well. It reads a given
  markdown file (or standard input) and produces a table of contents. The
  TOC can be generated  with or without links, in markdown format, based
  on any headings that may exist in the document, as well as their level.

## Usage Information

```bash
    ./mdtoc.py -h
```

    usage: MD TOC [-h] [-m {1,2,3,4,5,6}] [-M {0,1,2,3,4,5,6}] [-n] [-o OUTPUT]
                  [-s SEPARATOR] [-w WHITESPACE] [-x LEVEL]
                  [input]

    Generate a table of contents for a markdown document

    positional arguments:
      input                 The markdown file to read.

    optional arguments:
      -h, --help            show this help message and exit
      -m {1,2,3,4,5,6}, --min-indent {1,2,3,4,5,6}
                            Specify the minimum level of heading for which the
                            list items will be indented. Headings at or below this
                            level will not be indented and the rest of the heading
                            levels will be adjusted accordingly. The default is 1.
      -M {0,1,2,3,4,5,6}, --max-indent {0,1,2,3,4,5,6}
                            Specify the maximum level of heading for which the
                            list items will be indented. Headings above this level
                            will not be indented any further; Thus, specifying 0
                            flattens the list. The default is 6.
      -n, --no-links        Do not link the sections of the document to their list
                            items in the table of contents.
      -o OUTPUT, --output OUTPUT
                            The markdown file to write the table of contents to.
                            The default is standard output.
      -s SEPARATOR, --separator SEPARATOR
                            Specifies a string to be used as the separator between
                            the '*' character and the succeeding list item
                            (default: ' ').
      -w WHITESPACE, --whitespace WHITESPACE
                            Specify the characters used as whitespace before each
                            item. This is repeated or omitted depending on the
                            indentation level of each item. (default: ' ')
      -x LEVEL, --exclude LEVEL
                            Specify specific levels of heading to exclude from the
                            table of contents. This option can be repeated to
                            exclude multiple levels.

    Submit any bugs to https://github.com/mcb2003/md-toc-creater/issues/new
colortest 0.2.3
A simple script that checks for terminal true color support

=========
colortest
=========

|PyPI| |Pythons| |CI| |Codecov|

.. |PyPI| image:: https://img.shields.io/pypi/v/colortest.svg
  :alt: PyPI version
  :target: https://pypi.org/project/colortest/

.. |Pythons| image:: https://img.shields.io/pypi/pyversions/colortest.svg
  :alt: Supported Python versions
  :target: https://pypi.org/project/colortest/

.. |CI| image:: https://github.com/Julian/colortest/workflows/CI/badge.svg
  :alt: Build status
  :target: https://github.com/Julian/colortest/actions?query=workflow%3ACI

.. |Codecov| image:: https://codecov.io/gh/Julian/colortest/branch/master/graph/badge.svg
  :alt: Codecov Code coverage
  :target: https://codecov.io/gh/Julian/colortest

A simple script that checks for terminal true color support.
findme 0.2.2
A simple CLI for hypothesis.find

======
findme
======

|PyPI| |Pythons| |CI| |Codecov|

.. |PyPI| image:: https://img.shields.io/pypi/v/findme.svg
  :alt: PyPI version
  :target: https://pypi.org/project/findme/

.. |Pythons| image:: https://img.shields.io/pypi/pyversions/findme.svg
  :alt: Supported Python versions
  :target: https://pypi.org/project/findme/

.. |CI| image:: https://github.com/Julian/findme/workflows/CI/badge.svg
  :alt: Build status
  :target: https://github.com/Julian/findme/actions?query=workflow%3ACI

.. |Codecov| image:: https://codecov.io/gh/Julian/findme/branch/master/graph/badge.svg
  :alt: Codecov Code coverage
  :target: https://codecov.io/gh/Julian/findme


Usage
-----

``findme`` does a simple thing (entirely via Hypothesis):

.. code-block::

    $ findme integers x 'x > 1000'
    1001
quoridor 0.0.3
Quoridor Online Game
Requires Python: >=3.6

# Quoridor Online

Client and server to play the strategy board game **Quoridor**. It uses [pygame](https://www.pygame.org/news).

![](https://github.com/Quentin18/Quoridor-Online/blob/master/img/capture.png)

## Install
Requires: Python >=3.6.
To install, open a command prompt and launch:
```bash
pip3 install quoridor
```

## Use
To launch a server:
```bash
python3 -m quoridor.server [HOST] [PORT] [NUM_PLAYERS]
```
- HOST: IP address
- PORT: port number
- NUM_PLAYERS: number of players (2, 3 or 4)

To launch a client:
```bash
python3 -m quoridor.client [HOST] [PORT]
```
HOST and PORT must be the same as the server.

## Play
You can see the rules of the game [here](https://en.wikipedia.org/wiki/Quoridor):
- To move your pawn, use the four arrow keys
- To place a fence, click on the game board

At the end of the game, you can restart a game. Just click on the "Restart" button.

## Pathfinding algorithm
A pathfinding algorithm is used to check if a player is blocked or not. Thanks to the [python-pathfinding](https://github.com/brean/python-pathfinding) project.

## Contact
Quentin Deschamps: quentindeschamps18@gmail.com

## License
[MIT](https://choosealicense.com/licenses/mit/)