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Name: Bea Carbone

Type: User

Location: Boston, MA

Bea Carbone's Projects

a-syn_project

I developed this macro as a modification of the "arrange channels + stack to tiff" macro for a labmate of mine. It is fairly specific to her project, but a good backbone for further modification if need be. She needed to be able to take a stack of four channel, six slice z-stacked images and compress them halfway before performing dendrite selection and removing one of the channels. I set it up so she could do that and also retain the initial function of the macro. It might need some more troubleshooting, but it is definitely functional!

a-syn_project-dendriteselectonly

This is similar to the original a-syn project, I just removed the image compression step for easier recovery from human error.

ap_sliceanalysis

This macro was developed for analysis of organotypic slice culture

areatriplecoloc

This macro is designed to determine if two sets of ROI colocalize, find the overlapped areas, and determine if those two colocalizations assocaite with a third ROI set. It then determines the area of overlap between the overlapped area of the first two and the third and prints out the average therein.

arrangechannels-stacktotiff

this macro is intended to convert the z-stack, multichannel images from .lif files into individual tif files in a batch method.

createcomposite

This macro was done to try and streamline the process of taking any number of separate files for different color channels and combining them into the original images.

dendriteanalysis

This macro was originally developed by Lai Ding over at Harvard, there was an update that interfered with an externally referencing java command regarding directory organization, so I worked around it.

intellicount_colocalization

This macro was developed to take two images that had been analyzed using the MATLAB intellicount software and overlap them to determine colocalization by manual counting.

intellicount_traceadder

This macro was developed to be used in combination with the MATLAB program Intellicount. As Intellicount was initially developed for an in vitro culture, our use of it with an in vivo brain slice limited its efficacy and caused a significant number of missed puncta due to size exclusion, threshold, and a large range of intensities. This macro will take a single channel image with red tracings for the puncta and prompt selection of missed puncta using imageJ's polygon tool, allowing you to efficiently add ROI to an image and determine the area, intensity, and number of the missed puncta. It will also outline all selections in red in order to allow for consistent further analysis if so desired.

megamacro

This is a giant macro that was intended to streamline the flow of about 4-5 macros and have flexibility for multiple types of analysis. The language is the imagej macro language, which is a javascript derivative.

modifychannels

I wanted to make a macro that would allow you to change large, inconsistently constructed, groups of images in the same way using the same macro. For example, I have 60 four channel images (Cyan, Blue, Green, Red) that I want to be three channel images (Green, Red, Blue), but the blue channel is supposed to be green, the red is supposed to be blue, and the green is supposed to be red. This should do that.

roi_get

Another ImageJ macro designed to take a single or multichannel image and collect a ROI from it, save each channel to a separate image and

simple_functions

This is just a shortcut combining small macros I commonly use. Blinding images, selecting dendrite ROI's from a flat RGB image, unblinding images, and selecting a threshold for the R/G channels of each image.

spineintensityanalysis

a short macro to help automate intensity analysis between a spine head and shaft for a labmate

stepped-threshold-coloc

This was derived from the stepped thresholding analysis for the purpose of analyzing larger images (brain slices vs cell culture) and colocalizing the thresholded images.

steppedthreshold

Some of the guys in my lab needed a macro to see which threshold would be the best for each ROI, so this goes through 0-255 in iterations of 10

steppedthreshold-doublechannel

This is a derivative of the single channel ROI stepped threshold macro. This allows colocalization of two channels after quantifying puncta # and puncta avg area.

steppedthreshold-singlechannel

This is a macro derived from the one simply labeled "SteppedThreshold". This one only does one channel at a time (though is easily modifiable to repeat), and creates an array with comma separated values for puncta number and area. This is primarily used for very dense areas of puncta with unreliable background.

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