Skip to content

HenryCrosswell/Asymmetry_Macros

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

27 Commits
 
 
 
 
 
 

Repository files navigation

Overview


Custom ImageJ macros, for the quantification of both anterior and posterior neural folds (NFs) in mice.

Asymmetry_Macros

Disclaimer: These macros are to be used on confocal images, lower resolution could affect read-outs

Anterior neural fold quantification:

These macros must be used after the anterior NFs have been vertically orientated

  • Find Area
    • Finds the total area of a selected embryo
  • Find Maxima
    • Used for counting mitotic cells - fluoresce with proliferative antibody before analysis
    • Applys a median filter and finds maxima, to count pHH3
  • Six selections - for both pHH3 and total cell count
    • Make sure not to look at pHH3 layer prior to making selections
    • apply six selections using the macro, then follow instructions
  • Area difference
    • selects both NFs individually and measures their areas
  • Cfl1 quant
    • select an area that fits within both left-right NF
    • follow macros instructions

Posterior neural fold quantification

These macros must be used after the posterior NFs have been vertically orientated and surface sliced.

  • Deletion quantification

    • Used to measure Vangl2 deletion
    • follow instructions in the macro
  • Deviation map

    • Used to measure and visualise the percentage difference between overlapping and divergent volumes
    • Three different methods depending on the images you have.
  • Distance map

    • Finds the voxel distances between left and right NFs
    • Two different methods for different image types.
  • PNP select and quantification

    • 1-100 selection maker, makes 1% selections across the PNP and measures pixel intensity
    • Macro for outline, scans across the image until it hits a pixel, producing an outline
    • Overall intensity uses the above macro and measures intensity

About

Macros for ImageJ - towards the asymmetry project

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published