Embedded Files
Split channels and save Delta Vision (.dv) files as TIFF
Description:
> This macro processes all the .dv files in a directory and saves user-specified channels in the destination directory.
> Macro asks the user to select the source and destination directories and then prompts for the channel names (see below). Enter "none" if a channel does not exist, or if the user does not want to save a particular channel
> Macro saves channel names in the ImageJ Preference file (IJ_Prefs.txt) for retrieval during the next run.
Outline leading edge segment
This macro (available here) can be used to draw a segment ROI of user-specified thickness at the leading edge of a fluorescent cell, which can then be used to measure, e.g. mean fluorescence intensity in that segment. The macro was successfully used in the following article:
Bravo-Cordero JJ, Sharma VP, Roh-Johnson M, Chen X, Eddy R, Condeelis J, Hodgson L. Spatial regulation of RhoC activity defines protrusion formation in migrating cells. J Cell Sci. 2013 Aug 1;126(Pt 15):3356-69
A flow diagram of how to use the macro is described below.
Pipette assay macro
In a pipette assay, chemoattractant (e.g. EGF) is delivered through a pipette and the cell responds by extending a protrusion in the direction of the pipette. This macro was written to analyze the response of the cell (i.e. protrusion or retraction) along 16 radial directions (22.5 degrees apart) originating from the cell centroid to the cell periphery, where angle 0 degrees corresponds to the line joining the cell centroid to the pipette tip. The macro was successfully used in the following article:
Bravo-Cordero JJ, Sharma VP, Roh-Johnson M, Chen X, Eddy R, Condeelis J, Hodgson L. Spatial regulation of RhoC activity defines protrusion formation in migrating cells. J Cell Sci. 2013 Aug 1;126(Pt 15):3356-69
A flow diagram of how to use the macro is described below.
Combine all opened images horizontally
This macro runs Combine... command on two images at a time to stitch all the opened files, in the order that they are opened, or in the reverse order
Subtract uniform background
Description:
1. This macro subtracts the mean background fluorescence signal from each slice of a time-lapse stack.
2. User needs to draw an ROI representing the background area and make sure that the ROI does not pass through the real signal (i.e. a cell) in any of the slices.
3. The output is a new file with a name = original stack name + _bs
Copy specific files from one folder (and all its subfolders) to another location
> This macro copies files matching a user-defined pattern (e.g. all files ending with .xlsx and .pptx) from one location (source) to another location (destination).
> This macro operates on all the files in the folder and all of its subfolders.
> User needs to provide source directory (dirS), destination directory (dirD), and regex-based pattern to select the specific files to copy.
Note: This macro can be used to backup files from one location to another on a regular schedule (e.g. every week), by calling it inside ImageJ StartupMacros.txt file, or by a scheduler program (e.g. Task Scheduler, macro scheduler etc.)
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