v5.3.0 Release Notes

New Features

Complete Batch Processor and Real-Time Processor Redesign

The Batch Processor has been completely redesigned with a cleaner, more focused interface that reduces visual clutter while improving functionality. The previous interface displayed all controls simultaneously, creating unnecessary complexity even for simple batch operations. The new four-panel layout (Input, Output, Detection, and Measurements) presents only the relevant controls for each stage of batch configuration, making the interface more intuitive and less overwhelming. With the addition of live processing previews, the Detection panel now displays real-time overlays as each image is processed, allowing immediate visual verification of recipe performance without waiting for batch completion. Switch to the Measurements tab to see numerical results accumulate in real-time, with statistics updating after each processed image. This immediate feedback fundamentally changes batch workflow – you can now catch and correct issues within seconds rather than after processing hundreds of images. The redesign also unifies the Batch Processor and Real-Time Processor into a single interface. A simple mode toggle switches between traditional batch processing (manually queued images) and real-time monitoring (automatic processing of new images in a watched folder). The new interface delivers more capability with less complexity. Read the full Batch Processor documentation.

Fully Batchable Color-by-Measurement Analysis

Color By Measure functionality is now fully integrated into the Batch Processor, enabling automatic generation of measurement visualizations and statistical analyses across entire image datasets. This integration means you can now produce hundreds of color-coded measurement maps, histograms with fitted curves, and comprehensive statistical reports in a single batch run. All the customization options you’re familiar with from the Color By Measure tool – colormaps, colorbars, measurement selection, and curve fitting – are preserved and automatically applied to every image in your batch. The result is a complete measurement visualization workflow that scales from single images to thousands, with consistent formatting and publication-ready outputs. In addition to batch reports, you can now automatically generate individual output files for each processed image in a batch – measurement spreadsheets with complete feature data, Color By Measure overlay images maintaining all your colormap and colorbar settings, and measurement histograms with fitted curves and statistical parameters. These publication-ready outputs are intelligently named and organized by source image and measurement type, giving you immediate access to hundreds of consistently formatted graphics and data files without any manual post-processing. Read the full Color By Measure and Report Generator documentation.

Image Processor Quality-of-Life Improvements

Labels View in Simple Mode

Labels view is now available in Simple Mode, letting you display detection results with each feature uniquely colored, making it immediately obvious whether your segmentation is correctly separating adjacent objects. This view is available when working with zero or one visible layer. It is remembered as part of your recipe’s view configuration – if you save a recipe while in Labels view, it will automatically reopen in that same view next time. Any reports, batch outputs, or exported graphics generated from the recipe will display features in the same labeled format you used during development.

Recipe Management Shortcuts

New keyboard shortcuts put essential operations at your fingertips, dramatically reducing the time spent navigating menus and clicking buttons when building and refining recipes. Learn about all keyboard shortcuts here. E – Edit Recipe Step Delete – Remove Recipe Step C – Set Chapter R – Remove Chapter L – Set Layer M – Manage Layers D – Disable Here Down/Enable Here Up

Improvements

Base Package

• Introduced a new feature extraction capability to the Image Tile Extractor. Allows users to automatically extract features from images using a defined recipe. Designed to support advanced use cases in image processing and offers greater flexibility for downstream measurement and reporting tasks.
• Improved the measurement table positioning in the Image Processor for clearer results and easier access.
• Moved Math Process to top of Math menu in Image Processor.
• When changing the 2D labelling and connectivity preferences, a recipe loaded in the Image Processor will now re-run.
• Text overlay defaults in Color By Measure have been updated for improved user experience.
• The ‘Measurements’ table header was renamed from Measurement to Image to better reflect the structure of the ‘Per Field Measurement’ table.
• When opening an image with BioFormats, if the X and Y dimensions have different units, the value for the Y dimension is now adjusted to match the units of the X dimension.
• Alert uses to potential misalignment of companion-based measurements if image alignment is used during the same batch process as the measurements.
• “B/W Images” panel can now be hidden in the Session Processor to reduce clutter and allow more space for the Reference Images and Layers list.
• Spinner has been added to the measurement generation period during recipe load.
• Adjusted keyboard shortcuts for toggling Fill/Erase during manual editing in Manual Edit step and Session Processor: F (fill), E (erase), S (separate selection). Re-numbered shortcuts for edit tools in increasing order from top to bottom.
• Additional improvements to prevent hang-ups when closing windows on Mac.
• Can now set all colors and colormaps by clicking directly on the thumbnail, rather than the “…” button, which has been removed
• Loading spinners now display during large recipe loading and saving.
  

Spotlight Extension

• Spotlight and Snap will now catch and more intuitively report out-of-memory issues.
  

Deep Learning Extension

• Loading spinners will now appear when saving and loading session and model files that contain large deep learning models.
  

Live

• Added the ability to load custom camera adapters placed in “[MIPAR_ROOT]\capture\adapters\”.
  

3D Extension

• Added “Create from Files…” tool to File menu of 3D Toolbox for creating image stacks and reconstructions directly from 2D image files.
  

Bug Fixes

Base Package

• Fixed bug in the Batch Processor, when using cross-image alignment with a chosen recipe step that happens to be after the first specified layer.
• Fixed bug in the Batch Processor preventing accurate cross-image registration when registering based on a specified recipe step.
• Fixed bug where, if printing a report from the Batch Processor with a recipe that has no layers and the last step of the recipe is binary but the view saved into the recipe was saved from a prior grayscale step, the grayscale view settings would be erroneously applied to the recipe’s output binary image.
• Fixed bug preventing resuming of a Real-Time session if the watch folder is no longer accessible
• When MIPAR fails to open due to an error, error dialogs will remain displayed until they are closed.
• Fixed bug causing the labels overlay to flicker when loading a recipe in the Image Processor that defaults to labels view.
• Fixed bug with Batch Processor alignments that caused layer edges to be filled with selection.
• Fixed bug preventing the loading of OME Tiff images.
• Fixed Mac-specific issue where filenames containing 6 or more spaces caused report tables to display incorrectly with split headers and data.
• Fixed bug where Manual Edit step would occasionally fail to remember its saved viewing mode.
• Fixed bug in Grayscale Dilate/Erode Preview/Unpreview when the ‘show window’ option is turned on.
• Fixed incorrect overlay display when deleting recipe steps after disabling earlier steps containing Resize Image or Crop Image.
• Fixed bug with saving image in labels view out of Session Processor.
• Fixed bug where Session Processor could become corrupting while adding layers as sets of B/W images.
  

Spotlight Extension

• Fixed bug where Spotlight tiles were not recalculated after changing the “Apply to” image.
  

Live

• Fixed MIPAR Live bug preventing the saving of images captured from demo mock cameras.
• Improved error handling when a custom adapter errors on load.
• Fix bug in MIPAR Live where captured image scale factors were saved improperly if the units were not microns.
  

Hotfixes

5.3.0.1

Base Package

• Fixed overflow bug with labels view in recipes that result in a large number of features.
• Fixed error while saving grayscale image out of the Image Processor
• Fixed bug where “Thickness:” label would not show up in outline sub-mode of layers view in the Image Processor
• Fixed bug with setting colormap in layers view/labels submode in Simple Mode.
• Fixed bug with refreshing view when layers submodes have different settings in Simple vs. Detail mode.
  

Deep Learning Extension

• Significantly improved performance when running large models such as U-Nets with a depth of 4 or higher.
  

Spotlight Extension

• Improved memory management between Spotlight/Snap and the Deep Learning engine to access more memory when either is inactive.
  

5.3.0.2

Base Package

• Fixed a critical bug with Feature Measurement output in the Batch Processor after changes are made to the recipe.
• Resolved a Batch Processor performance issue where processing times increased exponentially with number of images processed. Overall processing speed during batch operations has been improved significantly. More performance enhancements are coming in a near-term update.
• Improved the performance of Measurement Table display in the Image Processor for recipes that contain large files such as images or Deep Learning models.
• Fixed bug where Ctrl/Cmd+C in the Image Processor could trigger the Set Chapter dialog.
• Fixed bug with deleting layers from some sessions in Session Processor.
• Fixed bug with moving a recipe Layer in a recipe with no Feature Measurements.
• Fixed bug that would prevent image measurements from being removed from a recipe.
• Added a ‘Saving’ spinner when embedding Batch Processor into a large recipe to prevent user interface perceived hang.
• Fixed bug in resuming session that would not load the Feature Outputs setting from the saved session.
• Fixed bug with step positioning that could occur when pasting recipe steps into fresh Image Processor.
• Fixed bug with sorting tables with text columns in Color By Measure.
  

Deep Learning Extension

• A spinner has been added when copying and pasting large models in the Apply Deep Learning recipe step.
  

3D Extension

• Fixed bug where Export Animation/Visualization would not close when using the “Close” button of the configuration window.
• Fixed Save As bug in the 3D Toolbox with reconstructions not created by the Create 3D Files from Images utility.
• Extended the ‘Saving’ spinner duration to prevent user interruptions during reconstruction saving.
• Save shortcuts changed to Ctrl/Cmd+S (for reconstructions) and Ctrl/Cmd+T (for image stacks)
  

5.3.0.3

Base Package

• Fixed bug in Histogram of Measurements that would prevent the histogram from displaying.
• Fixed bug when loading images that have an empty camera ‘Make’ tag.
• Fixed bug with Batch Processor display when launching on Mac.
  

5.3.0.4

Base Package

• Fixed bug with recipe replay after changing GPU Acceleration preference.
• Fixed bug with displaying images labels view when GPU Acceleration is turned on.
• Fixed bug while removing multiple recipe steps, with some steps before and others after the currently previewed step.
• Fixed bug with generating report from certain custom feature measurement that use text outputs.
• Fixed bug in the Batch Processor that would prevent calibration file loading.
• Fixed bug with removing layers in the Image Processor attached to some custom measurements.
• Fixed bug with certain image and recipe loading sequences in the Image Processor.
• Fixed bug with layer removals in the Session Processor which could be caused by prior layer additions.