Data

Tools

Indexes

Applications

Experiments

Open Source Science

bacterialsizescaling

Code relating to the scaling of bacterial cell size

https://github.com/cycelslab/bacterialsizescaling

Science Score: 65.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization cycelslab has institutional domain (www.iiserpune.ac.in)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Code relating to the scaling of bacterial cell size

Basic Info
  • Host: GitHub
  • Owner: CyCelsLab
  • License: gpl-3.0
  • Language: MATLAB
  • Default Branch: main
  • Size: 9.24 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created almost 4 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.md

Bacterial size scaling

Code relating to the scaling of bacterial cell size

Instructions for use (FM464 data)

  1. Download all contents of folder Code
  2. Open file SegmentationTest.m in MATLAB and run it.
  3. A figure window will open with cell overlays detected using the pipeline described in the paper. Select contours that are not correct.
  4. Output will be an overlay of detections and length and width of selected cell contours in pixel units.

Instructions for use (Phase Contrast)

  1. Download all contents of folder PhaseContrast
  2. Add the additional folders to the matlab path (bresenham/interparc/interpclosed)
  3. Open file PhaseSementationv3.m_ in MATLAB and run it.
  4. A figure window will open with cell overlays detected using the pipeline described in the paper.
  5. Output will be an overlay of detections and length and width of selected cell contours in pixel units.
  6. A final figure of a L & W plot and histogram of Lengths and widhts will show up.

List of toolboxes required

  1. Image Processing Toolbox
  2. Curve Fitting Toolbox
  3. Partial Differential Equation Toolbox

REFERENCE:

In case this code is used in any settings please refer to our paper that corresponds to this

Tanvi Kale, Dhruv Khatri and Chaitanya A Athale (2023) Allometry of Escherichia coli surface area with volume: effect of size variability, filamentation and division dynamics. Phys. Biol. 20 046007. DOI:10.1088/1478-3975/acdcda

Owner

  • Name: Cytoskeleton and Cell Shape (CyCelS)
  • Login: CyCelsLab
  • Kind: organization
  • Location: India

Self-Organization lab studying the role of collective mechanics and coupling to reaction networks that determine cell shape and division.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "The code is developed as part of a manuscript submitted for review. If you use the software please cite us as below."
authors:
  - family-names: Khatri
    given-names: Dhruv
 - family-names: Athale
    given-names: Chaitanya
    orcid: https://orcid.org/0000-0000-0000-0000
title: CyCelsLab/bacterialsizeScaling: Code for bacterial cell size analysis for allometry
version: image-analysis
date-released: 2022-12-13

GitHub Events

Total
Last Year