wisamreid / dendriteanalysis Goto Github PK

This macro is used to assess density and overlap of puncta along a dendrite.

The requirements are:
	-a folder with the dendrite ROI in subfolders by condition
	(ex: raw data/ctrl, raw data/DHA, raw data/Inos)
	-an empty folder for the dendrite traces produced by the macro
	-an empty folder for the results, autopopulates with subfolders
	for each condition
	-thresholds for the green and red channels

The images have to be: 
	-dendrite ROI selected along a marker (in the blue channel)
	-flattened RGB images
	-puncta of interest in red and green channels
	-dendrite length should be approx 20<x<40um

Nothing needs to be open when you start this macro.

A menu will pop up asking for several parameters:
	-green threshold
	-red threshold
	-area percent (how much % of an ROI should overlap w/
	the mask it is on to count as "co-localized")
	-pixel scale: dependent on image, different between 1024, 2048
	(specified in the image properties)
	-min and max puncta size in pixels

Once you input parameters here, it will automatically go to completion.

It produces:
	-a "summary.xls" that has all of the densities/colocalizations
	-a folder for each condition with the area of each puncta,
	the masks and puncta ROI information for each image within the condition
	-a dendrite tracing for each image

This is used frequently to analyze density of synapses on dendrites.

the "intensity ver" does everything that the original "dendrite analysis
macro-BC2018" does, it just adds the element of analyzing intensity of
signal in the original image.

It duplicates the original image prior to making it into a mask
and overlays the puncta ROI on the raw unmasked image to determine
pixel intensity density.

This is used for the cLTP project.