Panelize

Panelize is a script for arranging microscopy images into a grid with constant leveling for making figures. Multiple channels are supported with up to three-channel RGB merge. An arbitrary number of treatments is supported; each channel is scaled the same across all treatments. Adds a scalebar to the lower left image in the grid.

Download one of the packaged files from the "releases" section. Panelize requires that you have a JVM installed (tested on openjdk 21).

run panelize --help to see all options. You must at minimum supply the --n-rows and --mpp arguments to specify the number of rows you want to render and the number of microns per pixel for a scalebar.

You'll be promped for the image input for each row. Panelizer expects that the input images will be multi-channel images in a format that the bio-formats library can read and recognize as having multiple channels. If the images have multiple axial or time planes, only the final one will be used for display.

The final set of panels will be saved with a unique filename (which will be printed out) to the directory from which you ran the script.

If you want to tweak the scaling of the images, you should adjust the command line parameters scalesat and scaleundersat (run panelize --help to see the syntax for using these). If both these parameters are set to zero, in each channel, the images will be scaled between the min and max value appearing in that channel in any of the images. Setting these to a larger value will narrow the display range by the value supplied (in percent) from either the upper end (the scalesat parameter) or the lower end (scaleundersat), making the image appear brighter or the background dimmer, respectively.

Panelize is distributed under the MIT/X11 license (see LICENSE.txt for the full license).