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ZEISS Microscopy Knowledge Base

Using intensity range and visualization settings

This guide explains how to perform a correct intensity range setting and all the related adjustment operations needed to improve the image visualization.

Color Settings dialog showing color histograms with yellow and red overlays, diagonal curve and Gamma slider at 0,88

Color scalebar

arivis Vision4D User Interface shows a Color Bar for each channel present in the dataset (The channel visibility must be set ON). The Color Bar usage has several purposes, one of them is the Dynamic Range optimal mapping with respect to the Display Range.

By dragging the top and bottom slider along the Color Bar, the Dynamic Range can be freely set.

Vertical grayscale color bar with red top and bottom slider boxes and '65535' label at top

Right-Click on the slider. The top or bottom range value can be entered manually

The Dynamic range of each available channel can be adjusted independently.

Dialog labeled Enter value: with input showing 65535 and Apply and Cancel buttons

The Dynamic range changing does not influence the intensity measurements.

By pressing the Auto button, arivis Vision4D computes the best Dynamic range setting based on the active Z plane intensity distribution (Histogram).

AUTO label in blue above a small vertical slider icon

Cluster of faintly outlined rounded compartments on a black backgroundVertical grayscale color bar with red top and bottom slider boxes and '65535' label at topFluorescent microscopy image showing several bright ring-like cell outlines on a black backgroundVertical grayscale color bar labeled 65535 at top and 0 at bottom with a black-to-white gradient

The active Z plane can be changed using the Navigator panel controls. Please refer to the (arivis Vision4D Help) for more details.

Right-Click on the Auto button. A pop-up menu is displayed. Select the Global auto color item to compute the best Dynamic Range setting based on all the Z planes Histograms.

Right-click pop-up menu listing Scale mode, Auto color setup..., Auto color and Global auto color outlined in red

Color settings

Basically, the Color Settings panel allows to modify the Dynamic Range mapping as already shown above, but with a different approach. The range limits can be adjusted by dragging the lines at the beginning and end of the graph.

The target channel must be selected before moving the graph limits.

Color Settings panel, green channel selected, diagonal curve over green area, red arrows at left and right edges, 255

Gamma correction

Gamma is an important but seldom understood characteristic of virtually all digital imaging systems. It defines the non-linear relationship between a pixel's numerical value and its actual luminance. Without gamma, shades captured by digital devices wouldn't appear as they did to our eyes (on a standard monitor). Understanding how Gamma works can improve the image visualization and the details visibility. Our eyes do not perceive light the way the acquisition devices do. With an acquisition device, when twice the number of photons hit the sensor, it receives twice the signal (a "linear" relationship). That is not how our eyes work. Instead, we perceive twice the light as being only a fraction brighter — and increasingly so for higher light intensities (a "nonlinear" relationship).

Compared to an acquisition device, we are much more sensitive to changes in dark tones than we are to similar changes in bright tones. There is a biological reason for this peculiarity: it enables our vision to operate over a broader range of luminance. Otherwise, the typical range in brightness we encounter outdoors would be too overwhelming.

Below are some examples to clarify practically the Gamma concept:

Gamma = 1.0

A "linear" transfer function.

This is the default value.

Grayscale vertical ramp at left and right-side plot showing a straight blue diagonal transfer curve

Gamma = 2.0

A “non-linear" transfer function.

The dark part of the range is expanded.

Grayscale vertical ramp at left and right-side plot with a blue curve rising slowly then steeply

Gamma = 0,5

A “non-linear" transfer function.

The bright part of the range is expanded.

Grayscale vertical ramp at left and right-side plot with a blue curve rising quickly then flattening

The Gamma value can be modified dragging the gamma slider left or right or directly inputting the value into the text box.

The curve shape can be also modified.

Gamma = 1.0 - "linear".

Three bright green fluorescent circular shapes with soft blurred edges on a black backgroundColor Settings dialog showing a Gamma graph with green histogram, a Gamma: slider and a textbox displaying 1

Gamma = 0,5 - “non-linear" The bright part of the range is expanded.

Three bright green circular blobs connected on a black backgroundColor Settings dialog with Gamma tab selected, green channel, curve point, Gamma slider set to 0,56

Gamma = 1,98 - “non-linear" The dark part of the range is expanded.

Three connected green circular blobs on black background, blurredColor Settings dialog with Gamma tab, green channel curve, and Gamma slider set to 1,98

The Color Settings parameters can be exported / Imported as file.

Context menu showing Export... and Import...

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