Use Case Color Settings

A complete rework of our color setting having the typical workflows in mind which allows for fast and easy setting of intensities for single or several channels at the same time.
Now there is only one Color Settings panel, this includes the gamma, intensity thresholds and histogram functionalities in one fully interactive view.

Use case #1: Highlight nuclear stain in a 4 channel image

In this example we would like to highlight the nuclear stain in a 4 channel fluorescence image and we would also like to see the outline more clearly.
First, the min and max values can be set with a simple Auto scaling action. There are also a new options to exclude and outlier hot pixels. Additionally, you can use the color sliders’ in the 2D and 4D viewers to set the top and bottom intensities manually. Alternatively, you can use the Color Settings panel, which also shows you the histogram of the selected colors.

The next step is to highlight the lower intensity values using the gamma setting. There are several options to set the gamma value: Either by pulling the graph until it fits within the histogram representation or with a slider or via numerical input.

Hela cells stained with Hoechst, AuroraB-A488 (Kinetochore components), Tubulin-A568 (Spindle fibers), ACA-A647 : Anti Centromer antibodies  Image courtesy of Carl ZEISS microscopy: ZEISS AxioObserver 7 with Colibri 7 illumination, deconvolved with ZEN Blue 2.5

An interactive histogram and a graphical representation of the gamma value supports the best settings to display intensities for any channel independently.

In addition, a spline curve can be set and interactively pulled to result in any custom curve.

All these settings are stored for reuse in other data sets, or sharing with other users. A list of previously saved or loaded presets, are available for quick switching between custom settings.

New custom defined color gradients are freely interactively designed for an easy to use interface.

The new color gradient manager in preferences, allows for organization and control, along with setting favorites for shortcuts or to use them also for objects.

Use case #2: Display volumes of vesicles in color code

In this use case, the aim is to differentiate the different volume of vesicles by color, so here we use a color code for the volume.

The objects were generated by our Analysis Pipeline can be colored according to measurements as well as any custom features to see differences in the 4D Viewer using a color code. The objects and channels, any color gradient can be used, and either standard or custom gradients.

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