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Import Bioformats Image Tool

This tool enables you to use Bioformats as an integrated library for reading and writing image file formats. It is capable of parsing both pixels and metadata for a large number of formats. It achieves this by converting proprietary microscopy data into an open standard called the OME data model. With Bioformats, you can read proprietary formats and convert them. For example, it is possible to load simple images you can import, such as camera images or more complex images, such as a light microscope image with overlays, to ZEN core.

Parameter

Description

File Name

The path and filename of the table to be loaded

Click on to open the file browser and select the desired file.

For more information, see ZEN Connect.

Import ZEN Connect Project Tool

Parameter

Description

Filename

The path and filename of the project to be loaded.

Click on to open the file browser and select the desired project.

For more information, see Importing a ZEN Connect Project.

For more information, see ZEN Connect Module.

ZEN Connect Tool

Within a ZEN Connect project, you manage your data in a project structure tree combined with the viewer.

Parameter

Description

Project / Layers

The ZEN Connect tool provides a Layers view and a Tree view of image data that you have acquired for the ZEN Connect project. Every image that you have acquired for the ZEN Connect project is listed. As you acquire or import more image data, the new image data will be listed in the views.

Change Opacity

Adjusts the opacity of detected objects.

Align

Activates the alignment process for the selected data, see Activating the Alignment Process.

Align System

Activates the alignment process for the current microscope session, see Activating the Alignment Process.

New Session

Creates a new session.


Context Menu

Displays the context menu for ZEN Connect, see Context Menu.

For more information, see ZEN Connect.

ZEN Connect Renderer Tool

Parameter

Description

Tree View tool

For more information, see ZEN Connect Tool.

Color Style

Controls the color format of the export. Select RGB (color) or Intensity (black and white).

RGB Color

Based on the RGB (Red-Green-Blue) color model. Be aware that color files may be up to three times as large as intensity files.

Intensity

Images are saved in 8-bit format.

Export Format

Selects the format for the exported file.

CZI image (Single Channel)

Exports the image as a Carl Zeiss Image file. CZI files are not limited in size. The images are exported in a single channel CZI.

CZI image (Multi-Channel)

Exports the image as a Carl Zeiss Image file. CZI files are not limited in size. The images are exported as a multi-channel CZI.

Note that the resulting image might look different when reopened in ZEN than it does in ZEN Connect.

Burn in Data Bar

Activated: Burns the currently configured data bar into the exported image.

Rotation

Rotates the view to the desired orientation. Drag the slider, or in the text field, type in the value.

Pixel Size

Sets the pixel size of the export. The smaller the pixel size, the more disk space your export will take. The options Low, Medium and High only have an effect, if several images are exported as a single image.

Smallest

Sets pixel size of the finest image, i.e. the smallest pixel size.

Medium

Calculates and sets the pixel size to the log average of finest and coarsest image (i.e. 10^(0.5*(log(fine)+log(coarse)).

Largest

Sets pixel size of the coarsest image, i.e. the largest pixel size.

Custom

Sets a custom pixel size which can be entered in the input field.

Width (px)

Sets the width to directly alter the export pixel count and export area (the pixel size is unchanged).

Height (px)

Sets the height to directly alter the export pixel count and export area (the pixel size is unchanged).

Width (µm)

Displays the full width of the export area in µm.

Height (µm)

Displays the full height of the export area in µm.

Approx. Data Size

Displays an approximation for the data size of the exported image. The actual file size after export may be less, depending on compression of some file formats.

For more information, see Exporting Images from a ZEN Connect Project.

Measurements Tool

Parameter

Description

Measurement Tools


Distance

Allows the user to add two points to measure a distance.


Angle

Allows the user to add three points to measure an angle.


Area

Allows the user to draw a polygon contour to measure an area.


Circle

Allows the user to draw a circle to measure a diameter.

Measurement table

Value

Displays the measured value.

Type

Displays the icon of the measurement type.


Visibility

Toggles the visibility of each measurement.

Name

Displays the name of each measurement.


Delete

Deletes the currently selected measurement.

Create Table

Creates and opens a table document with the current measurement values.

Flip/Mirror Tool

Parameter

Description


Horizontally

Mirrors the image in horizontal direction.


Vertically

Mirrors the image in the vertical direction.

Shear Tool

Parameter

Description

Enable

Activated: Activates the shearing mode and displays the three shearing pins in the image.

Reset Shearing Pins

Resets the pins to the default location.

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