Giter VIP home page Giter VIP logo

fluorescenceexclusion.jl's Introduction

FluorescenceExclusion.jl

Documentation Build Status

Fluorescence Exclusion Microscopy is a quantitative imaging method for measuring cell volume that relies on the exclusion of a dye by cells in chambers with a known height. This is a Julia implementation inspired by the "1.4 Data Analysis" section in Cadart et al.

[¹]: Cadart, C., Zlotek-Zlotkiewicz, E., Venkova, L., Thouvenin, O., Racine, V., Le Berre, M., Monnier, S., & Piel, M. (2017). Chapter 6 - Fluorescence eXclusion Measurement of volume in live cells. In Thomas Lecuit (Ed.), Methods in Cell Biology (Vol. 139, pp. 103–120). Academic Press. http://www.sciencedirect.com/science/article/pii/S0091679X16301613

Installation

Until this package is registered in the General repository, the easiest way to install the latest stable version is to add https://github.com/tlnagy/TNRegistry as follows:

using Pkg
pkg"registry add [email protected]:tlnagy/TNRegistry.git"

Then installation is as easy as

using Pkg
Pkg.add("FluorescenceExclusion")

fluorescenceexclusion.jl's People

Contributors

github-actions[bot] avatar tlnagy avatar

Watchers

avatar avatar avatar

fluorescenceexclusion.jl's Issues

Tag first version

  • test flatfield correction code
  • test pillar identification
  • edge-detection tests for cell identification
  • test tracking code

Switch to interpolation to find true minimum signal for each cell

As mentioned in 57677ae, despite my best efforts there is still heterogeneity between pillars. That is, even after normalization, the pillars have different values, which means there are multiple true minimum signals. The proper fix is to calculate a true minimum signal per cell by interpolating between the pillars.

Volume error propagation should take the error in determining the cell's area into account

Currently, the only error that is propagated is the error associated with estimating the median signal of the locality, which I calculate here:

FluorescenceExclusion.jl/src/particles.jl

Line 70 in a08f8e9

push!(medbkgs, median(bkg) ± (1.253 * std(bkg) / sqrt(length(bkg))))

The other substantial source of error could be from how correctly I call the "area" of the cell. Perhaps the best approach there is to resample the edge pixels and see how much the signal varies.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.