MIPAR User Manual

v4.5.0 Release Notes


New Features


Spotlight Extension

  • We are excited to introduce MIPAR Spotlight. Integrated into the Image Processor, Spotlight enables the next generation of feature detection.
  • Spotlight behaves like any other detection Recipe step, so MIPAR Clean-up, Morphology and detection mask handling is still accessible. Recipes that contain a Spotlight step are fully batchable using the Batch Processor or the Real Time Processor

Snap Tool, powered by MIPAR Spotlight

  • We are excited to introduce MIPAR Snap into the Manual Edit and Session Processor workflows. Snap is powered by Spotlight which enables the tool to detect anything the user points to or draws a box around.
  • Snap offers Fast and Accurate modes; Fast enables lower resource requirements in exchange for lower detection performance in some applications. Accurate is much more resource intensive but offers unparalleled edge accuracy.

Session Processor Redesign

  • Improved the user experience inside the Session Processor by increasing the size of the image and improving the organizations of the editing tools.
  • Introduced the Snap tool, enabled by the Spotlight Extension.
  • Improved the interface layout for both session review workflows as well as model training workflows.
  • Improved layer management capabilities.
  • Redesigned the editing tool buttons.
  • Introduced ‘Separate Selection’ which will automatically keep any annotations discrete.

Manual Edit Redesign

  • Improved the user experience inside the Manual Edit recipe step by increasing the size of the image and improving the organizations of the editing tools.
  • Introduced the Snap tool, enabled by the Spotlight Extension
  • Redesigned the editing tool buttons
  • Introduced ‘Separate Selection’ which will automatically keep any annotations discrete.

Batch Report Generation

  • Reports can now be generated from the Batch Processor, Real-Time Processor and the Session Processor, enabled by the Report Generation Extension.
  • Batch reports can include a user selected representative image, all images or no images.
  • Introduced ‘Compress Images’ option to reduce the file size of the output report documents.
  • Introduced ‘Aggregate Stats’ option to compile measurement statistics across the entire batch.
  • Introduced ‘Save Images’ option which will save images from the batch report as individual image files.


Improvements

Base Package

  • Custom Measurement Manager is hidden while editing or adding a new custom measurement to reduce interface clutter.
  • Improved window maximization for all major apps.
  • Eliminated the Cancel button in the status bar when it was not effective.
  • Added ‘Edition’ to Help>About.
  • Improved the close window experience to reduce question dialogs.
  • When immediately stopping a session (or resuming a session after, for example, a power outage) in the Batch or Real-Time Processor, partial results from the image being processed will get cleaned up from the session folder.

Report Extension

  • Renamed Aggregate Statistics to Summary Statistics in the Report Generator window and output report file.


Fixes

Base Package

  • Fixed handling of proprietary image formats in the Session Processor when opening a session from the Batch Processor.
  • Fixed bug with loading and editing a recipe that contains a Custom Measurement that uses the Text feature measurement.
  • In the Image Processor, selecting Save Reference Image and Save Current Image will no longer update the image name in the user interface with the new name.
  • Fixed bug with removing a Layer in the image processor after editing a downstream step.
  • Fixed bug in the Color by Measure window that sometimes prevents the update of which feature is highlighted on the overlay image when selecting a new feature.
  • Fixed bug that was writing custom measurements mapped to text as a number in the report file.
  • Fixed bug where a portable session saved from the Batch or Real-Time Processors where the recipe has no crop or resize steps or with no batch AOI tracking would rely on the location of the original image files.
  • Fixed bug with the resumption of portable sessions with measurements if the portable session has been moved, where the resumed measurements would be placed in a new folder alongside the previous measurements folder.
  • Fixed bug in the Real Time Processor that makes a second session folder if first image is processed alone.
  • Fixed bug with editing a recipe with Feature Measurements to add a Companion Area measurement.
  • Fixed bug with Preferences GPU dropdown not updating after replacing the video card on the system.
  • The Cross-Correlate pre-processing step will no error when the companion image is flat. Instead, a warning dialog will appear and a blank image will be returned instead.
  • Stomata Cell 2 Template recipe loads the appropriate recipe.
  • Improved examples of using intercepts measurements in custom measurements.
  • Fixed bug where the custom measurement was not being displayed as ‘Mapped’ when selected in the Custom Measurement Manager.
  • Improved the Stats dropdown in the Local Measurement window to eliminate scrollbars.
  • Fixed bug preventing the effect of the “Strength” parameter for local thickness measurements using the “Smooth” skeleton. Recipes built prior to this version will continue to give the same results.
  • Fixed bug with skeleton trimming for local thickness measurements using the “Classic” skeleton. This may cause recipes built prior to this version to give different results if they used trimming on Classic skeletons.
  • Changed default colormap for Grayscale>False Color viewing mode from grayscale to parula.
  • Fix bug preventing the clearing of a manual edit mask in the Auto Segmentation step.
  • Disabled the Accept button when no annotations are added to the Auto Segmentation step.
  • Fixed bug in FFT Filter step that would disable the Annular>Inner Frequency input.
  • Prevent the ability to drag-and-drop recipes into the Batch and Real-Time Processors inappropriately when the session is processing or paused.
  • Prevent the ability to drag-and-drop images into the Batch Processor inappropriately when the session is processing.
  • Disable the button to resume a session in the Real-Time Processor when a session is already running.

Deep Learning Extension

  • Fixed bug that allowed the Batch Processor to launch the Session Processor while a Deep Learning training was active.

3D Extension

  • Fixed the appearance of the Stop button in the 3D Toolbox.
  • Enabled middle-click pan control to the 3D Manual Edit window, available even in the middle of a draw operation.
  • Enabled use of scroll wheel to operate image slider control when using zoom and pan in 3D Toolbox, 3D Manual Edit, and 3D Merge Layers.


Hotfixes

4.5.0.1

Base Package

  • Fixed bug preventing the display and update of histograms in the Color-by-Measure window on load and when selecting a cell in both another column and another row from the previously-selected cell.
  • Fixed bug that would enable Save Image and Save All Images without any layers in the Session Processor.
  • Fixed bug with scale bar not printing by selecting Save Image or Save All Images in the Session Processor.
  • After opening the Activation window through an app’s Help menu, closing the Activation window will no longer automatically shut down MIPAR.
  • Replacing a color image file in Load Companion Image with another will no longer reset the channel operation.
  • Fixed bug that would cause recipe execution to stop if an error was encountered with the status bar.
  • Prevented the status bar from grabbing focus after the progress has started.
  • Spotlight Extension*
  • Fixed bug where Spotlight after Call Original and Crop Image would incorrectly use the un-cropped condition on grayscale images.

Report Extension

  • Fixed bug when the “sum” statistic could be omitted from some reports.

4.5.0.2

Base Package

  • Fixed bug with closing software which could leave licenses unreleased.

4.5.0.3

Base Package

  • Fixed bugs relating to scale factor reversion during undo operations in the Image Processor.
  • Fixed bug where portable Sessions saved on Windows would not open on Mac and vice-versa.

4.5.0.4

Base Package

  • Fixed bug preventing the viewing of sessions built with Spotlight in the Session Processor on a system without a Spotlight license
  • Fixed bug with creating custom image measurement based on a statistic of a feature measurement which depends on memory image input.
  • Fixed bug preventing the deactivation of hardware acceleration.

Express Package

  • Fixed bug allowing the opening of recipes without layers in MIPAR Express

Spotlight Extension

  • Fixed bug allowing the use of recipes built with Spotlight to perform dynamic scale factor calculation on a system without a Spotlight license

API

  • Fixed the use of very old recipes through the Python and REST APIs

4.5.0.5

Base Package

  • Fixed bug in Session Processor preventing the use of Save All Images when a layer other than the first is selected.
  • Fixed bugs preventing the loading of recipes with dynamic calibration.
  • Fixed bug when generating measurements from the Session Processor.
  • Fixed error that occurs with Adjust Contrast, Auto Mode if the adjustment value takes the auto-determined values outside the image’s dynamic range.

Deep Learning Extension

  • Fixed bug that could soft-lock the AI Session Processor after accepting error dialog about trying a DL training with one layer.

4.5.0.6

Base Package

  • Improved error handling on Mac when opening an image from a folder which the system has not been granted permission to access.
  • Improved reading of indexed png files.
  • Fixed the generation of measurements when performed from the Color by Measurements window.
  • Fixed bug where Manual Edit steps added in “Erase” mode would reopen in “Fill” mode.
  • Improved error handling during execution of custom measurements. Specifically, when a missing or wrong type memory or companion image is passed in.
  • Improved error handling when removing companion images with a dependent image or feature path length measurement added.
  • Fixed bug preventing the use of image dimension measurements inside a custom measurement formula
  • Fixed bug where network extension licenses would not properly remain checked out while MIPAR is open on a workstation.
  • Fixed bug where some recipes failed to load when custom measurements are applied to an empty image.
  • Fixed bug that would prevent custom measurements with ‘Var’ in the name from printing in the Color by Measure window.

Report Extension

  • Fixed bug which could result during certain PDF displays.

Checkpoint

  • Fixed bug where DOCX file was not removed before results export.
  • Fixed a bug when checking for corrupted MIPAR Checkpoint projects.

New Features


Spotlight Extension

  • We are excited to introduce MIPAR Spotlight. Integrated into the Image Processor, Spotlight enables the next generation of feature detection.
  • Spotlight behaves like any other detection Recipe step, so MIPAR Clean-up, Morphology and detection mask handling is still accessible. Recipes that contain a Spotlight step are fully batchable using the Batch Processor or the Real Time Processor

Snap Tool, powered by MIPAR Spotlight

  • We are excited to introduce MIPAR Snap into the Manual Edit and Session Processor workflows. Snap is powered by Spotlight which enables the tool to detect anything the user points to or draws a box around.
  • Snap offers Fast and Accurate modes; Fast enables lower resource requirements in exchange for lower detection performance in some applications. Accurate is much more resource intensive but offers unparalleled edge accuracy.

Session Processor Redesign

  • Improved the user experience inside the Session Processor by increasing the size of the image and improving the organizations of the editing tools.
  • Introduced the Snap tool, enabled by the Spotlight Extension.
  • Improved the interface layout for both session review workflows as well as model training workflows.
  • Improved layer management capabilities.
  • Redesigned the editing tool buttons.
  • Introduced ‘Separate Selection’ which will automatically keep any annotations discrete.

Manual Edit Redesign

  • Improved the user experience inside the Manual Edit recipe step by increasing the size of the image and improving the organizations of the editing tools.
  • Introduced the Snap tool, enabled by the Spotlight Extension
  • Redesigned the editing tool buttons
  • Introduced ‘Separate Selection’ which will automatically keep any annotations discrete.

Batch Report Generation

  • Reports can now be generated from the Batch Processor, Real-Time Processor and the Session Processor, enabled by the Report Generation Extension.
  • Batch reports can include a user selected representative image, all images or no images.
  • Introduced ‘Compress Images’ option to reduce the file size of the output report documents.
  • Introduced ‘Aggregate Stats’ option to compile measurement statistics across the entire batch.
  • Introduced ‘Save Images’ option which will save images from the batch report as individual image files.


Improvements

Base Package

  • Custom Measurement Manager is hidden while editing or adding a new custom measurement to reduce interface clutter.
  • Improved window maximization for all major apps.
  • Eliminated the Cancel button in the status bar when it was not effective.
  • Added ‘Edition’ to Help>About.
  • Improved the close window experience to reduce question dialogs.
  • When immediately stopping a session (or resuming a session after, for example, a power outage) in the Batch or Real-Time Processor, partial results from the image being processed will get cleaned up from the session folder.

Report Extension

  • Renamed Aggregate Statistics to Summary Statistics in the Report Generator window and output report file.


Fixes

Base Package

  • Fixed handling of proprietary image formats in the Session Processor when opening a session from the Batch Processor.
  • Fixed bug with loading and editing a recipe that contains a Custom Measurement that uses the Text feature measurement.
  • In the Image Processor, selecting Save Reference Image and Save Current Image will no longer update the image name in the user interface with the new name.
  • Fixed bug with removing a Layer in the image processor after editing a downstream step.
  • Fixed bug in the Color by Measure window that sometimes prevents the update of which feature is highlighted on the overlay image when selecting a new feature.
  • Fixed bug that was writing custom measurements mapped to text as a number in the report file.
  • Fixed bug where a portable session saved from the Batch or Real-Time Processors where the recipe has no crop or resize steps or with no batch AOI tracking would rely on the location of the original image files.
  • Fixed bug with the resumption of portable sessions with measurements if the portable session has been moved, where the resumed measurements would be placed in a new folder alongside the previous measurements folder.
  • Fixed bug in the Real Time Processor that makes a second session folder if first image is processed alone.
  • Fixed bug with editing a recipe with Feature Measurements to add a Companion Area measurement.
  • Fixed bug with Preferences GPU dropdown not updating after replacing the video card on the system.
  • The Cross-Correlate pre-processing step will no error when the companion image is flat. Instead, a warning dialog will appear and a blank image will be returned instead.
  • Stomata Cell 2 Template recipe loads the appropriate recipe.
  • Improved examples of using intercepts measurements in custom measurements.
  • Fixed bug where the custom measurement was not being displayed as ‘Mapped’ when selected in the Custom Measurement Manager.
  • Improved the Stats dropdown in the Local Measurement window to eliminate scrollbars.
  • Fixed bug preventing the effect of the “Strength” parameter for local thickness measurements using the “Smooth” skeleton. Recipes built prior to this version will continue to give the same results.
  • Fixed bug with skeleton trimming for local thickness measurements using the “Classic” skeleton. This may cause recipes built prior to this version to give different results if they used trimming on Classic skeletons.
  • Changed default colormap for Grayscale>False Color viewing mode from grayscale to parula.
  • Fix bug preventing the clearing of a manual edit mask in the Auto Segmentation step.
  • Disabled the Accept button when no annotations are added to the Auto Segmentation step.
  • Fixed bug in FFT Filter step that would disable the Annular>Inner Frequency input.
  • Prevent the ability to drag-and-drop recipes into the Batch and Real-Time Processors inappropriately when the session is processing or paused.
  • Prevent the ability to drag-and-drop images into the Batch Processor inappropriately when the session is processing.
  • Disable the button to resume a session in the Real-Time Processor when a session is already running.

Deep Learning Extension

  • Fixed bug that allowed the Batch Processor to launch the Session Processor while a Deep Learning training was active.

3D Extension

  • Fixed the appearance of the Stop button in the 3D Toolbox.
  • Enabled middle-click pan control to the 3D Manual Edit window, available even in the middle of a draw operation.
  • Enabled use of scroll wheel to operate image slider control when using zoom and pan in 3D Toolbox, 3D Manual Edit, and 3D Merge Layers.


Hotfixes

4.5.0.1

Base Package

  • Fixed bug preventing the display and update of histograms in the Color-by-Measure window on load and when selecting a cell in both another column and another row from the previously-selected cell.
  • Fixed bug that would enable Save Image and Save All Images without any layers in the Session Processor.
  • Fixed bug with scale bar not printing by selecting Save Image or Save All Images in the Session Processor.
  • After opening the Activation window through an app’s Help menu, closing the Activation window will no longer automatically shut down MIPAR.
  • Replacing a color image file in Load Companion Image with another will no longer reset the channel operation.
  • Fixed bug that would cause recipe execution to stop if an error was encountered with the status bar.
  • Prevented the status bar from grabbing focus after the progress has started.
  • Spotlight Extension*
  • Fixed bug where Spotlight after Call Original and Crop Image would incorrectly use the un-cropped condition on grayscale images.

Report Extension

  • Fixed bug when the “sum” statistic could be omitted from some reports.

4.5.0.2

Base Package

  • Fixed bug with closing software which could leave licenses unreleased.

4.5.0.3

Base Package

  • Fixed bugs relating to scale factor reversion during undo operations in the Image Processor.
  • Fixed bug where portable Sessions saved on Windows would not open on Mac and vice-versa.

4.5.0.4

Base Package

  • Fixed bug preventing the viewing of sessions built with Spotlight in the Session Processor on a system without a Spotlight license
  • Fixed bug with creating custom image measurement based on a statistic of a feature measurement which depends on memory image input.
  • Fixed bug preventing the deactivation of hardware acceleration.

Express Package

  • Fixed bug allowing the opening of recipes without layers in MIPAR Express

Spotlight Extension

  • Fixed bug allowing the use of recipes built with Spotlight to perform dynamic scale factor calculation on a system without a Spotlight license

API

  • Fixed the use of very old recipes through the Python and REST APIs

4.5.0.5

Base Package

  • Fixed bug in Session Processor preventing the use of Save All Images when a layer other than the first is selected.
  • Fixed bugs preventing the loading of recipes with dynamic calibration.
  • Fixed bug when generating measurements from the Session Processor.
  • Fixed error that occurs with Adjust Contrast, Auto Mode if the adjustment value takes the auto-determined values outside the image’s dynamic range.

Deep Learning Extension

  • Fixed bug that could soft-lock the AI Session Processor after accepting error dialog about trying a DL training with one layer.

4.5.0.6

Base Package

  • Improved error handling on Mac when opening an image from a folder which the system has not been granted permission to access.
  • Improved reading of indexed png files.
  • Fixed the generation of measurements when performed from the Color by Measurements window.
  • Fixed bug where Manual Edit steps added in “Erase” mode would reopen in “Fill” mode.
  • Improved error handling during execution of custom measurements. Specifically, when a missing or wrong type memory or companion image is passed in.
  • Improved error handling when removing companion images with a dependent image or feature path length measurement added.
  • Fixed bug preventing the use of image dimension measurements inside a custom measurement formula
  • Fixed bug where network extension licenses would not properly remain checked out while MIPAR is open on a workstation.
  • Fixed bug where some recipes failed to load when custom measurements are applied to an empty image.
  • Fixed bug that would prevent custom measurements with ‘Var’ in the name from printing in the Color by Measure window.

Report Extension

  • Fixed bug which could result during certain PDF displays.

Checkpoint

  • Fixed bug where DOCX file was not removed before results export.
  • Fixed a bug when checking for corrupted MIPAR Checkpoint projects.

4.5.0.7

Base Package

  • Fixed bug which caused an incorrect image Y-dimension measurement.


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