Image Analysis

The group Image Analysis provides different options to analyze images in single or batch mode. The measurement data can be embedded in the image, saved in a *csv-datalist, or saved as label image.

Analyze

This function is applicable only for one image: This must be selected in the Input tool. The measurement data are embedded in the image.

Analyze to File

This function is applicable only for one image: This must be selected in the Input tool. The measurement data is stored in a *csv list and is not embedded into the image.

The following file types are supported:

Parameter	Description
Data Folder	Folder where the *csv-data lists will be stored.
Base Name	Name of the data list.

Analyze Batch

This function allows the analysis of all images in a folder.

The function Analyze Batch can only be applied to images with the file type *czi.

The measured data are embedded in each original image.

Parameter	Description
Image Folder	Folder of the *czi images to be measured.

Analyze Batch to File

This function allows an analysis of all images in a folder. The measured data are stored in a *csv list and not embedded into the image.

The following file types are supported:

Parameter	Description
Image Folder	Folder of the images to be measured.
Data Folder	Folder where the *csv-data lists will be stored.
Base Name	Name of the data list.
Append Data	Activated: For each class, an accumulated csv-data list is stored with the measurement data of all images. Deactivated: For each image, one data list is stored per class.

Analyze to Label Image

The image processing functions Analyze to Label Image labels images based on an existing image analysis setting and the parameters which you select in the Parameters section.

Parameter		Description
Setting		Displays image analysis settings in the drop-down list.
Initialization		Initializes the output image.
–	One channel	Creates a one channel output image.
–	One channel and copy first	Creates a one channel output image and copies the content of the first channel.
–	One channel per class	Creates an output image with one channel per region class.
–	One channel per class and copy	Creates an output image with one channel per region class and copies the content of the original channels of each class.
–	All referenced channels	Creates all channels referenced in the image analysis setting.
–	All referenced channels and copy	Creates all channels referenced in the image analysis setting and copies the content of the original image.
–	Copy all Channels and Label all	Creates an output image containing each channel of the input image and overlays each channel the masks of all classes defined in the image analysis setting.
Label Mode		Selects the mode of labels applied to the image.
–	Region - Pixel Type Maximum	Labels the region with the maximum value of the pixel type.
–	Region - Label Value	Labels the region with the value specified by the Label Value slider/ input field.
–	Region - Region ID	Labels the region with the region ID.
–	Region - Region ID Color	Labels the region with the region ID color.
–	Region - Region Class ID	Labels the region with the region class ID.
–	Region - Region Class Color	Labels the region with the region class color.
–	Contour - Pixel Type Maximum	Draws a contour with the maximum value of the pixel type.
–	Contour - Label Value	Draws a contour with the value specified by the Label Value slider/ input field.
–	Contour - Region ID	Draws a contour with the color defined by the region ID.
–	Contour - Region ID Color	Draws a contour with the color defined by the region ID color.
–	Contour - Region Class ID	Draws a contour with the color defined by the region class ID.
–	Contour - Region Class Color	Draws a contour with the color defined by the region class color.
–	Contour2 - Pixel Type Maximum	Draws a double contour with the value defined by the maximum value of the pixel type.
–	Contour2 - Label Value	Draws a double contour with the value specified by the Label Value slider/ input field.
–	Contour2 - Region ID	Draws a double contour with the color defined by the region ID.
–	Contour2 - Region ID Color	Draws a double contour with the color defined by the region ID color.
–	Contour2 - Region Class ID	Draws a double contour with the color defined by the region class ID.
–	Contour2 - Region Class Color	Draws a double contour with the color defined by the region class color.
Pixel Type		Selects the pixel type for the output image.
–	8 Bit B/W	Creates an 8 bit black and white output image.
–	16 Bit B/W	Creates a 16 bit black and white output image.
–	24 Bit RGB	Creates a 24 bit colored output image.
–	48 Bit RGB	Creates a 48 bit colored output image.
–	32 Bit B/W Float	Creates a 32 bit black and white image.
Label Value		Selects the label value.

Analyze to Label Image Batch

The image processing functions Analyze to Image Batch labels images based on an existing image analysis setting and the parameters which you select in the Parameters section.

Parameter		Description
Setting		Displays image analysis settings in the drop-down list.
Image Folder		Selects the folder of the images.
Initialization		Initializes the output image.
–	One channel	Creates a one channel output image.
–	One channel and copy first	Creates a one channel output image and copies the content of the first channel.
–	One channel per class	Creates an output image with one channel per region class.
–	One channel per class and copy	Creates an output image with one channel per region class and copies the content of the original channels of each class.
–	All referenced channels	Creates all channels referenced in the image analysis setting.
–	All referenced channels and copy	Creates all channels referenced in the image analysis setting and copies the content of the original image.
–	Copy all Channels and Label all	Creates an output image containing each channel of the input image and overlays each channel the masks of all classes defined in the image analysis setting.
Label Mode		Selects the mode of labels applied to the image.
–	Region - Pixel Type Maximum	Labels the region with the maximum value of the pixel type.
–	Region - Label Value	Labels the region with the value specified by the Label Value slider/ input field.
–	Region - Region ID	Labels the region with the region ID.
–	Region - Region ID Color	Labels the region with the region ID color.
–	Region - Region Class ID	Labels the region with the region class ID.
–	Region - Region Class Color	Labels the region with the region class color.
–	Contour - Pixel Type Maximum	Draws a contour with the maximum value of the pixel type.
–	Contour - Label Value	Draws a contour with the value specified by the Label Value slider/ input field.
–	Contour - Region ID	Draws a contour with the color defined by the region ID.
–	Contour - Region ID Color	Draws a contour with the color defined by the region ID color.
–	Contour - Region Class ID	Draws a contour with the color defined by the region class ID.
–	Contour - Region Class Color	Draws a contour with the color defined by the region class color.
–	Contour2 - Pixel Type Maximum	Draws a double contour with the value defined by the maximum value of the pixel type.
–	Contour2 - Label Value	Draws a double contour with the value specified by the Label Value slider/ input field.
–	Contour2 - Region ID	Draws a double contour with the color defined by the region ID.
–	Contour2 - Region ID Color	Draws a double contour with the color defined by the region ID color.
–	Contour2 - Region Class ID	Draws a double contour with the color defined by the region class ID.
–	Contour2 - Region Class Color	Draws a double contour with the color defined by the region class color.
Pixel Type		Selects the pixel type for the output image.
–	8 Bit B/W	Creates an 8 bit black and white output image.
–	16 Bit B/W	Creates a 16 bit black and white output image.
–	24 Bit RGB	Creates a 24 bit colored output image.
–	48 Bit RGB	Creates a 48 bit colored output image.
–	32 Bit B/W Float	Creates a 32 bit black and white image.
Label Value		Selects the label value.
Format		Selects the format of the output image. You can save your image(s) as: czi png czi and png

Analyze Interactive Batch

This function allows the interactive analysis of all images in a folder. If steps of the image analysis are marked as interactive in the image analysis setting, this function opens the Image Analysis Wizard with these steps. You can then adjust your analysis for each of the images. If you deselect one of the interactive steps during the process, this step will not be shown for the analysis of the following images. The image analysis setting remains unchanged by the changes made during Analyze Interactive Batch.