The Unified_Merge Plugin

This plugin allows to create an image which may contain one or several individual channels in grayscale alongside a colored merge of several channels.

Sample output from the Unified_Merge plugin

To illustrate the purpose of this plugin, let´s consider a sample output in the figure above. The hyperstack used as the source image was made of three different channels (DiC, mCherry::H2A.Z, and GFP::Polo). From that source, the plugin generated an image composed of four panels side by side: the three leftmost panels depict the individual channels, in grayscale; the rightmost panel depicts a composite colored image of all three channels merged together.

When the plugin is called, you´re presented with a settings dialog lile the one depicted below. The settings are organized in several sections.

Settings dialog for the Unified_Merge plugin

General settings

This section contains the following settings:

Orientation
This defines whether the panels will be placed next to each other, with the merged panel on the right (Horizontal), or one on top of another, with the merged panel at the bottom Vertical).
Separator width
If this option is enabled, the panels will be separated by a white line whose width (in pixels) can also be specified.
Font size
This is the size of the font used to display the labels. The value can range from 8 to 24.
Copy original overlay only once
If the original hyperstack contains an overlay and this option is enabled, the overlay will only be carried over to the first panel (leftmost panel or top panel, depending on the orientation setting) of the final image. If this option is not enabled, the overlay will be duplicated as needed to be carried over to all panels.

Frame settings

Settings in this section are only meaningful for hyperstacks containing several time-frames (t-frames).

First frame/Last frame
Those settings allow to create an image containing only a subset of the t-frames from the original hyperstack. First frame is the 1-based offset of the first t-frame to include in the resulting image; Last frame is the 1-based index of the last t-frame to include. The default behavior is to include all t-frames (i.e. First frame defaults to 1 and Last frame defaults to the number of t-frames).
Show labels on all frames
If this option is selected, channel labels will be visible on all t-frames.
Show labels in this frame
If the previous option is not selected, this setting indicates which t-frame will carry the channel labels.
Show time labels
If this option is enabled, each t-frame will carry a time indicator on the top left corner of the image.
Interval
If enabled, this option allows to specify the time elapsed (in seconds) between each t-frame; otherwise the plugin will attempt to find that information in the metadata of the original hyperstack.
Offset first frame
If this option is enabled and the First frame option is set to anything else than its default value of 1, time indicators will be shifted so that the first actual t-frame to be included in the resulting image will have a time of 0.
Use 00:00 format
If enabled, time indicators will be displayed with a semi-colon to separate minutes from seconds. Otherwise the default format is to display h, m, and s units.

Channel settings

The settings dialog will contain one channel settings section for each channel in the original hyperstack.

Name
This is the name which will be used to label the channel.
Color
This is the color to use to colorize the channel in the merged image. The channel label will also be displayed in the indicated color.
Show individual image
If this option is enabled, the channel will be displayed on a panel of its own, in the leftmost (or top, depending on the Orientation setting) part of the image.
Show merged image
If this option is enabled, the channel will appear on the merged panel, on the rightmost (or bottom, depending on the Orientation setting) part of the image.

Examples

The first figure on the top of this page was an example of an image with all channels dusplayed both individually and on the merge panel (Show individual image and Show merged image options enabled for all three channels.

The image below is an example of a simple merge, with all channels only displayed as part of the merged image. This image was generated by enabling the Show merged image option and disabling the Show individual image option for all three channels.

Example of a simple merge

Finally, the image below is an example of a more complex merge, where only the GFP::Polo channel is shown on a panel of its own, while the merged panel contains all three channels. This image was generated by enabling the Show merged image option on all three channels, but enabling the Show individual channel option only on the GFP::Polo channel. Note also that the Orientation option was set to “Vertical”.

Example of a more elaborated merge