The official repository of iGEM Paris Bettencourt team's software tools.

Overview

iGEM_ParisBettencourt21

The official repository of iGEM Paris Bettencourt team's software tools.

Cell counting

There are two programs dedicated to the cell counting from the GFP images obtained from the experiments.

The first python program(gfpminicell_count.py) involves the following image processing techniques

  • cleaning by border stripping
  • gray-scaling
  • gaussian blurring
  • binary thresholding for preparing the processed image

The second program(cell_count.py) involves additional sharpening and thresholding techniques before gaussian blurring in order to capture the full contours of different sized images. So in sequence, the image goes through cleaning -> gray-scaling -> filter-convolved sharpening -> binary thresholding -> gaussian blurring -> final binary thresholding.

For the final counting, a procedure called contour mapping from OpenCV is used and the corresponding contours are counted as the number of cells seen on the processed images.

Example Images

There are two folders dedicated to store images for each of the two programs described above:

  • Cells folder consists of sample images containing both mother and minicells and
  • Minicells folder has Green Fluorescent Protein (GFP) images of only minicells

Running the program for cell counting

We need a basic python environment and preferably Miniconda or Anaconda as they help keep all the packages modular

  • In order to install the required packages for this program, run the following command that uses python3-pip: pip3 install -r requirements.txt

  • For minicell counting (from images that has only minicells filtered), put them in the Minicells folder and run the following command python gfpminicell_count.py -i GFPMinicells/3.png

  • For cell counting from images that includes both mother and minicells, put them in the Cells folder and run the following command in the main folder containing the .py file python cell_count.py -i Cells/mgfp01.JPG

    Note: Cells/mgfp01.JPG and Minicells/1.png are just sample images from the example folders, they could be replaced by GFP microscopic images with the corresponding relative path to the files

Interpreting results

The program outputs:

  • Original border-cropped image: "Cleaned-original image"

Example: GFPMinicells/3.png

  • Final processed image on which the contours are mapped and counted: "Contour-ready image"

Example: Contour-ready3.png

  • The number of cells counted in the GFP image: "cell-count" (Also in the window-caption of the processed image) Example above: cell-count is 18

Another (Mini)cells count example

Example: Cells/mgfp01.JPG

Image uploader

The image_uploading_bot.py script is dedicated to automated web navigation. It uses the selenium python extensions to

  • Upload a set of images from a local folder to the igem servers
  • Store the data of the uploaded files for accessible wiki editing

minicell producing culture models

There are two version of simulation for culture of minicell producing strains:

  • version 1 is an algorithmic approach for low number of cells
  • version 2 is another approach using approximation of partial differential equations

version 1

On the first version called minicell_bioproduction_model_v1.py different simulation where implementated according to different assumptions. The ouput are graphs of cell growing and minicell/mothercell counting

Owner
Abhay Koushik
I am an Engineer, Artist, and Researcher exploring Neurosciences and Psychology.
Abhay Koushik
Writeup of NilbinSec's participation in the Winja CTF for c0c0n 2021

Winja-CTF-c0c0n-2021-Writeup NilbinSec's participation in the Winja CTF for c0c0n 2021 This repo covers NilbinSec's participation in the Winja CTF dur

1 Nov 15, 2021
Pylexa - Artificial Assistant made with Python

Pylexa - Artificial Assistant made with Python Alexa is a famous artificial assistant used massively across the world. It is a substitute of Alexa whi

\_PROTIK_/ 4 Nov 03, 2021
This Curve Editor, written by Jehee Lee in 2015

Splines Abstract This Curve Editor, written by Jehee Lee in 2015, is a freeware. You can use, modify, redistribute the code without restriction. This

Movement Research Lab 8 Mar 11, 2022
A python script to make leaderboards using a CSV with the runners name, IDs and Flag Emojis

SrcLbMaker A python script to make speedrun.com global leaderboards. Installation You need python 3.6 or higher. First, go to the folder where you wan

2 Jul 25, 2022
Probably the best way to simulate block scopes in Python

This is a package, as it says on the tin, to emulate block scoping in Python, the lack of which being a clever design choice yet sometimes a trouble.

88 Oct 26, 2022
Trashselected - Plugin for fman.io to move files that has been selected in fman to trash

TrashSelected Plugin for fman.io to move files that has been selected in fman to

1 Feb 04, 2022
mrcal is a generic toolkit to solve calibration and SFM-like problems originating at NASA/JPL

mrcal is a generic toolkit to solve calibration and SFM-like problems originating at NASA/JPL. Functionality related to these problems is exposed as a set of C and Python libraries and some commandli

Dima Kogan 102 Dec 23, 2022
Install packages with pip as if you were in the past!

A PyPI time machine Do you wish you could just install packages with pip as if you were at some fixed date in the past? If so, the PyPI time machine i

Thomas Robitaille 51 Jan 09, 2023
A python trivium implemention

A python trivium implemention

tnt2402 1 Nov 12, 2021
Parser for the GeoSuite[tm] PRV export format

Parser for the GeoSuite[tm] PRV export format This library provides functionality to parse geotechnical investigation data in .prv files generated by

EMerald Geomodelling 1 Dec 17, 2021
✔️ Create to-do lists to easily manage your ideas and work.

Todo List + Add task + Remove task + List completed task + List not completed task + Set clock task time + View task statistics by date Changelog v 1.

Abbas Ataei 30 Nov 28, 2022
Simple tooling for marking deprecated functions or classes and re-routing to the new successors' instance.

pyDeprecate Simple tooling for marking deprecated functions or classes and re-routing to the new successors' instance

Jirka Borovec 45 Nov 24, 2022
Wordle-solve - Attempting to solve wordle

Wordle Solver Run with python wordle_beater.py. This hardmode wordle solver take

Tom Lockwood 42 Oct 11, 2022
Blender addon to import images as meshes

ImagesAsMesh Blender addon to import images as meshes. Inspired by: ImagesAsPlanes Installation It's like just about every other Blender addon. Downlo

Niccolo Zuppichini 4 Jan 04, 2022
Simple Wayland HotKey Daemon

swhkd Simple Wayland HotKey Daemon This project is still very new and I'm making new decisions everyday as to where I should drive this project. I'm u

Aakash Sen Sharma 407 Dec 30, 2022
Nmap script to detect a Microsoft Exchange instance version with OWA enabled.

Nmap script to detect a Microsoft Exchange instance version with OWA enabled.

Luciano Righetti 27 Nov 17, 2022
No more support server flooding with questions about unsupported hosting.

No more support server flooding with questions about unsupported hosting.

3 Aug 09, 2021
Visual Python and C++ nanosecond profiler, logger, tests enabler

Look into Palanteer and get an omniscient view of your program Palanteer is a set of lean and efficient tools to improve the quality of software, for

Damien Feneyrou 1.9k Dec 26, 2022
Integration of CCURE access control system with automation HVAC of a commercial building

API-CCURE-Automation-Quantity-Floor Integration of CCURE access control system with automation HVAC of a commercial building CCURE is an access contro

Alexandre Edson Silva Pereira 1 Nov 24, 2021
🐍 This snake helps you reconnect the Web, with RSS feeds!

This snake helps you reconnect the Web, with RSS feeds! RSSerpent is an open-source software that create RSS feeds for websites that do not provide an

211 Dec 08, 2022