https://github.com/shuyib/cell-explorer-tool

An image explorer tool that uses ipywidgets and image manipulation in Pillow to look for and refine features in a image. This is mostly pitched on cell biology, cytopathology and histopathology.
https://github.com/shuyib/cell-explorer-tool

cell-biology cytopathology histopathology image-processing interactive ipynb ipywidgets medical-imaging mybinder pathology

Last synced: about 2 months ago
JSON representation

An image explorer tool that uses ipywidgets and image manipulation in Pillow to look for and refine features in a image. This is mostly pitched on cell biology, cytopathology and histopathology.

• Host: GitHub
• URL: https://github.com/shuyib/cell-explorer-tool
• Owner: Shuyib
• License: mit
• Created: 2020-04-07T12:00:28.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2022-09-17T09:39:23.000Z (over 2 years ago)
• Last Synced: 2024-04-16T03:50:50.284Z (9 months ago)
• Topics: cell-biology, cytopathology, histopathology, image-processing, interactive, ipynb, ipywidgets, medical-imaging, mybinder, pathology
• Language: Jupyter Notebook
• Homepage:
• Size: 729 KB
• Stars: 4
• Watchers: 2
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# cell-explorer-tool

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Shuyib/cell-explorer-tool/master)

An image explorer tool to look for and refine features from microscopy images from cell biology projects, cytopathology projects, histopathology projects and other image related experiments in a reproducible way. You can open an image preferably JPG format, adjust the coordinates of the image, save the image and parameters used to change the image, rename the image file and write description with the app in the *.ipynb. The tool will give you another more refined image resized to 500 by 500 with a TXT file and a JSON file. 

Project structure

---

The project has the following files:

* LICENSE - an MIT License 

* README.md - an explanation of what the project is about, what kind of data is used and the output.

* image-processing-raw-final.ipynb - has documented code to process images at most 4 for some reason.

* requirements.txt - Has python libraries in specific versions e.g ipywidgets == 7.5.1

**Running on Docker guide**  

---

Build docker image

```bash

docker build -t cell-exp:v0 .

```

Run the Docker image

```bash

docker run -it -p 2323:2323 cell-exp:v0

```