Modality

To handle the out-of-focus planes correctly, it is important to know how exactly the image sequence has been acquired. Select the proper microscopic modality from the combo box.

Pinhole size

Depending on the Modality setting, set the pinhole/slit size value and choose the proper units.

Magnification

Specify magnification of the objective used to capture the image sequence.

Numerical Aperture

Enter the numerical aperture of the objective.

Immersion Refractive Index

Enter the refraction index of the immersion medium used. Predefined refraction indexes of different media can be selected from the pull-down menu.

Calibration

Enter the image calibration in μm/px.

Output

Check if you need to create new document. Otherwise the clarifying is applied to the original image.

Channels

Select which channels will be clarified and which will be denoised. You can also adjust the emission wavelength. To revert the changes, click .

Preview

If checked, the clarifying preview is shown in the original image.

OK

Confirms the settings and performs the clarifying.

Cancel

Closes the window without executing any process.

Modality

To handle the out-of-focus planes correctly, it is important to know how exactly the image sequence has been acquired. Select the proper microscopic modality from the combo box.

Magnification

Specify magnification of the objective used to capture the image sequence.

Numerical Aperture

Enter the numerical aperture of the objective.

Refraction Index

Enter refraction index of the immersion medium used. There are some predefined refraction indexes of different media in the nearby pull down menu.

Calibration

Enter the image calibration in μm/px.

Channels

Image channels produced by your camera are listed within this table. You can decide which channel(s) shall be processed by checking the check boxes next to the channel names. The emission wavelength value may be edited (except the Live De-Blur method).

Note

Brightfield channels are omitted automatically.

Channels

Select on which channels the denoising will be performed.

Create new document

Check this item if creating a new document after denoising is required. Otherwise the denoising is applied to the original image.

Preview

If checked, the denoising preview is shown in the original image.

OK

Confirms the settings and performs the denoising.

Cancel

Closes the window without executing any process.

Network

Choose Automatically (default) selects the method automatically by analyzing the image. Correlated Noise is used for removing the line noise typically made by the Confocal Ax resonant scanner. Uncorrelated Noise is used for removing the common point noise.

Channels

Select on which channels the denoising will be performed.

Create new document

Check this item if creating a new document after denoising is required. Otherwise the denoising is applied to the original image.

Preview

If checked, the denoising preview is shown in the original image.

OK

Confirms the settings and performs the denoising.

Cancel

Closes the window without executing any process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.eai file) or from a database (From Explorer).

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI channels

Specifies the name of the newly created channels.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Cancel

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.cai file) or from a database (From Explorer).

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI channels

Specifies the name of the newly created channels.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Cancel

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.sai file) or from a database (From Explorer).

Multi-Smooth

This feature is used to smooth out multiple binaries at once.

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI binaries

Specifies the name of the newly created binaries.

Advanced

Reveals post-processing tools and restrictions used for enhancing the results of the neural network.

For more information about how each feature works, please see Measurement Features.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Cancel

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.oai file) or from a database (From Explorer).

Also, Pre-trained AI networks are available:

• 10x_nuclei_fl.oai

• 20x_nuclei_fl.oai

  AI classifier for nuclei detection of all cells (standard).

• 10x_nuclei_fl_apoptosis_cytotoxicity_all.oai

  AI classifier for nuclei detection of all cells (apoptotic and dead analysis).

• 10x_nuclei_fl_apoptosis_cytotoxicity_dead.oai

  AI classifier for detection of apoptotic and dead nuclei of cells.

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI binaries

Specifies the name of the newly created binaries.

Advanced

Reveals post-processing tools and restrictions used for enhancing the results of the neural network.

For more information about how each feature works, please see Measurement Features.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Cancel

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.eai3d file) or from a database (From Explorer).

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI channels

Specifies the name of the newly created channels.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Close

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.cai3d file) or from a database (From Explorer).

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI channels

Specifies the name of the newly created channels.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Close

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.sai3d file) or from a database (From Explorer).

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI binaries

Specifies the name of the newly created binaries.

Advanced

Reveals post-processing tools and restrictions used for enhancing the results of the neural network.

For more information about how each feature works, please see Measurement Features.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Close

Closes the window without executing the process.

Document channels

Channels on which the neural network will be run.

Source AI channels

Lists channels on which the network was trained (also shown in Details...). If a “ - ” symbol is shown and Trained AI is highlighted red, it indicates that the path to the neural network is incorrect or the network is corrupt. If both the Source AI channels and Document channels are highlighted red, there is a mismatch in the channel selection (i.e. less or more channels are selected or there is an RGB / standard channel mismatch).

Trained AI

Selects the trained network - either from a file (From File, click Browse to locate the *.oai3d file) or from a database (From Explorer).

Details...

Opens metadata associated with training of the currently selected neural network.

Created AI binaries

Specifies the name of the newly created binaries.

Advanced

Reveals post-processing tools and restrictions used for enhancing the results of the neural network.

For more information about how each feature works, please see Measurement Features.

Preview

Shows a preview of the current settings applied to the opened image.

OK

Confirms the settings and runs the process.

Close

Closes the window without executing the process.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Source AI channels

Low light signal channels used for neural training.

Ground truth channels

High light signal channels used for neural training. AI will be trained to reconstruct the ground truth channels using information in source channels.

Options

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Convert from

Source channels used for AI training.

Convert to

Ground truth channels for AI training. AI will be trained to convert the source channels into the ground truth channels.

Options

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Source AI channels

Source channels used for AI training.

Ground truth binaries

Binary layers used as a ground truth for AI training. AI will be trained to segment the source channels as in the ground truth binary layers.

Options

Cutout area

To exclude a certain area from the training, drag a binary layer into the Cutout area. Image under this binary area will be cut out from the training.

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Source AI channels

Source channels used for AI training.

Ground truth binaries

Binary layers used as a ground truth for AI training. AI will be trained to segment the source channels as in the ground truth binary layers.

Options

Cutout area

To exclude a certain area from the training, drag a binary layer into the Cutout area. Image under this binary area will be cut out from the training.

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Source AI channels

Low light signal channels used for neural training.

Ground truth channels

High light signal channels used for neural training. AI will be trained to reconstruct the ground truth channels using information in source channels.

Options

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Convert from

Source channels used for AI training.

Convert to

Ground truth channels for AI training. AI will be trained to convert the source channels into the ground truth channels.

Options

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Source AI channels

Source channels used for AI training.

Ground truth binaries

Binary layers used as a ground truth for AI training. AI will be trained to segment the source channels as in the ground truth binary layers.

Options

Cutout area

To exclude a certain area from the training, drag a binary layer into the Cutout area. Image under this binary area will be cut out from the training.

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Training data

...

Opens a dialog where you can choose a dataset train image file or change the path to a different file.

Removes the path to the dataset train image.

Add files

Opens a dialog where you can add another dataset train image file.

Channels

Source AI channels

Source channels used for AI training.

Ground truth binaries

Binary layers used as a ground truth for AI training. AI will be trained to segment the source channels as in the ground truth binary layers.

Options

Cutout area

To exclude a certain area from the training, drag a binary layer into the Cutout area. Image under this binary area will be cut out from the training.

Iterations

Number of AI training iterations.

Output

Name in Explorer

Input the name for your AI used in the NIS.ai Explorer.

Save

Specify the output file where the AI will be stored.

Save graph screenshot

Saves a screenshot of the training graph, so that it can be examined after the training is finished and the progress window is closed. This is useful when training multiple networks by a macro.

Add to Queue

Adds the current training into a queue so that it can be executed later ( Train Queued) via NIS.ai Explorer on the current workstation. These symbols are shown before the training name indicating the queued training.

Add to Cluster

(requires: Ai Image Processing) (requires: Local Option) (requires: Compute Cluster Support)

Sends the current training to the computer cluster system running HTCondor. System automatically selects a suitable computer which is turned on and ready to process the job. If such a computer is not available, the job will wait until such computer is available. When there are more suitable computers, the system chooses the most powerful one. Then it will start processing the task (“Running” is indicated in NIS.ai Explorer). When the task is finished, “Complete” is shown. If your computer is not involved in the cluster, it can be turned off during the cluster processing. These symbols are shown in NIS.ai Explorer before the training name indicating the clustered training.

Note

Make sure that the image being processed is located on a shared storage and not your local hard drive.

Train

Executes the AI training.

Cancel

Closes the window without executing the AI training.

Help

Opens this help page.

Draw/Edit

Pointing Tool

Pointing tool for selecting objects.

Undo

Standard undo action.

Redo

Standard redo action.

Separate

Detects standalone objects that are connected together and isolates them.

Fill Holes

Fills the holes inside binary objects.

Clean

Removes the small objects from the binary.

Smooth

Smooths the binary contours.

Invert

Inverts the current binary.

Clear Screen

Clears all binaries in the image.

Settings

Opens the Editor Settings dialog where you can manage custom and predefined presets. Each preset can be adjusted to contain just the tools the user needs (checked items). The order of the tools can be changed by clicking and dragging a tool up/down in the list. Shortcut for each tool or function can be changed by clicking on the shortcut and typing in the new key combination. Once you finish editing your shortcut list, use Save or Save As... to save it as a preset. Any presets can be selected from the Preset drop-down menu. The selected preset can also be imported (Import ) or exported ( Export) from/to an .msegpreset file. To remove a preset from the preset list, use Remove.

A list of other useful shortcuts is shown on the right.