Maximum Intensity Projection (MIP)

The mip module is run together with the other processing modules and will create MIPs for key modules that are run. For example, if running both deskew and decon, MIPs will be made for both. The subfolder created by mip will contain subfolders indicating which input images were used to create them (e.g., a decon subfolder). Inside this folder will be files that end with mip_x, mip_y, and mip_z. The dimension in the file name is the axes over which the images have been projected.

Modules Enabled	MIPs Created
mip only	input images
flatfield	flatfield
crop	crop
crop + flatfield	crop
(crop and/or flatfield or none) + deskew	deskew
decon + mip	input images & decon
flatfield + decon	flatfield & decon
crop +/- flatfield + decon	crop & decon
(crop and/or flatfield or none) + deskew + decon	deskew & decon
(crop and/or flatfield or none) + decon-first	deskew_after_decon
(crop and/or flatfield or none) + decon-first + deskew	deskew_after_decon + deskew
(crop and/or flatfield or none) + decon-first + deskew + decon	deskew_after_decon + deskew + decon

Viewing MIPs

2D MIPs are very useful for screening data, but in general, should not be used for downstream analysis (use the appropriate processed image folder of 3D images). To quickly look at MIPs in ImageJ, use the option under File > Import > Image Sequence.... This will open a dialog box that allow for selecting the directory of images to load in. The directory will be something like /path/to/experiment/mip/deskew/. By default, the importer will attempt to open all images in the folder. This begins by opening the first image in the folder, and then excluding any subsequent files that are not the same size. In the case of mip folders, this will lead to importing only _x files. To get only the files of interest, the Filter: dialog can be used to select files. For example, to select the z projections, input _z in the filter dialog.

More complex filtering of imported images is also possible using regular expressions. In ImageJ, .* is a wildcard, and the complete regular expression must be enclosed in parentheses. For example, to load in y projections of only channel zero, use (ch0.*_y) in the filter dialog. When the filter dialog box is changed, the number of images to be loaded automatically changes (shown in the Count: dialog). If the value is --- or otherwise does not make sense, there is likely a typo in the regular expression.

Usage

Pipeline: Configuration File

In the configuration file, simply specify which axes to create (true) or ignore (false). In general, set all values to true.

"mip": {
    "x": true,
    "y": true,
    "z": true
}

Command Line Example

When directly using the mip module on the command line, you must specify the input and output files. You should also input the axes to project over (-x -y -z). The following example makes MIPs in all three dimensions for a deskewed image. Specify the pixel sizes to output properly scaled projections.

mip -x  -y  -z  -p 0.104 -q 0.21462536238843902 -o /path/to/experiment/mip/deskew/scan_Cam1_ch0_tile0_t0000_deskew_mip.tif /path/to/experiment/deskew/scan_Cam1_ch0_tile0_t0000_deskew.tif

MIP Options

mip: generates a maximum intensity projection along the specified axes
usage: mip [options] path

Allowed options:
  -h [ --help ]                      display this help message
  -x [ --x-axis ]                    generate x-axis projection
  -y [ --y-axis ]                    generate y-axis projection
  -z [ --z-axis ]                    generate z-axis projection
  -p [ --xy-rez ] arg (=0.104000002) x/y resolution (um/px)
  -q [ --z-rez ] arg (=0.104000002)  z resolution (um/px)
  -o [ --output ] arg                output file path
  -b [ --bit-depth ] arg (=16)       bit depth (8, 16, or 32) of output image
  -w [ --overwrite ]                 overwrite output if it exists
  -v [ --verbose ]                   display progress and debug information
  --version                          display the version number