Custom ImageJ macros, for the quantification of both anterior and posterior neural folds (NFs) in mice.
Disclaimer: These macros are to be used on confocal images, lower resolution could affect read-outs
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
These macros must be used after the posterior NFs have been vertically orientated and surface sliced.
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Deletion quantification
- Used to measure Vangl2 deletion
- follow instructions in the macro
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Deviation map
- Used to measure and visualise the percentage difference between overlapping and divergent volumes
- Three different methods depending on the images you have.
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Distance map
- Finds the voxel distances between left and right NFs
- Two different methods for different image types.
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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