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3D Toolbox
3D Toolbox
Requires 3D Extension The 3D Toolbox is used for visualizing and editing Image Stacks as well as visualizing, editing, and quantifying 3D Reconstructions. Reconstructions can be exported to other visualization applications such as commercial Avizo and open source…
3D Toolbox
Getting Started » Tutorials » 3D Toolbox
Overview of 3D Reconstruction Shows the workflow for creating, processing, visualizing, and measure a 3D Reconstruction. Downloads You may download the below assets to use as learning tools and follow this tutorial. ⇩ Raw Dataset ⇩ Calibration Data ⇩…
v3.4.1 Release Notes
Release Notes » v3.4.1 Release Notes
Improvements Added a preference to increase the amount of memory available for opening specialty file formats with Bio-Formats Removed “Enter Dimensions” entry from Crop menu in 3D Toolbox since functionality is present in Crop > Draw Bug…
v3.3.2 Release Notes
Release Notes » v3.3.2 Release Notes
New Features Slice-by-Slice Measurements in 3D Slice-by-Slice Measurements can now be made in the 3D Toolbox. This enables any of the Feature Measurements to be made from all X-Y slices, where each slice’s feature labeling is based on the full 3D labeling.…
Layout
3D Toolbox » Layout
Below are labeled screenshots of the 3D Toolbox which reveals the layouts of and purpose behind each user interface element. Layout #1: Recon (recommended when working with a reconstruction) Shows the Reconstruction side only. Used when working with a…
v4.4.0 Release Notes
Release Notes » v4.4.0 Release Notes
New Features Pause/Resume Batch Processing We are pleased to introduce a new Save/Resume feature to our Batch Processor and Real-Time Processor, which allows users to pause active batch or real-time processing, and resume at a later time. Previous sessions…
v3.2.0 Release Notes
Release Notes » v3.2.0 Release Notes
New Features Choose Format When Saving Multiple Images You can now choose between the following formats when using “Save All Images” from the Post Processor and Deep Learning Trainer: TIFF PNG JPEG BMP HDF4 Re-designed Pattern Mapping …
Real-Time Processor
Real-Time Processor
The Real-Time Processor is similar to the Batch Processor, but used for applying a Recipe to multiple images, every time a new image is added to a folder being “watched”. Any global or feature measurements added to the recipe will be output into the save…
Tutorials
Getting Started » Tutorials
Watch video tutorials on how to use many of MIPAR’s features: Overview Image Processor Batch Processor Session Processor AI Session Processor 3D Toolbox
Getting Started
Getting Started
Welcome to the MIPAR User Manual! This manual is meant to complement the various tutorials and 1-on-1 training sessions available on the MIPAR website. It offers an overview of the each application, and provides a comprehensive description of the Image…
v3.0.5 Release Notes
Release Notes » v3.0.5 Release Notes
Bug Fixes Addressed bug where resizing Manual Edit windows can cause editing tools to crash Fixed bug where Manual Edit would crash when “interruptible” while running a batch which contained a Crop Image step Fixed bug where white background would…
Supported Formats
Getting Started » Supported Formats
2D Formats The following 2D image formats are supported for use in the Image Processor, Batch Processor, Real-Time Processor, and Session Processor: TIF JPG BMP PNG GIF Bio-Formats (over 150 formats ) Requires downloading the Bio-Formats package and placing…
Introduction
Getting Started » Introduction
MIPAR is a revolutionary image analysis software, capable of identifying and measuring features from nearly any image one can capture. Our users have shown it to be perhaps the most the efficient and flexible image processing software on the planet. Through five…
v3.4.2 Release Notes
Release Notes » v3.4.2 Release Notes
Improvements BP and RTP will now save intermediate session files during batch, such that sessions can be reviewed and/or merged followed a batch cancellation In Simple Mode in the IP, “Measurements” is now written beside the Measurements Panel…
v4.5.0 Release Notes
Release Notes » 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,…
v4.2.0 Release Notes
Release Notes » v4.2.0 Release Notes
New Features Recipe Templates MIPAR now ships with a fully interactive environment to browse and try over 80 pre-built recipe templates. Sort by category, search, and even watch videos on the available templates. Each recipe also offers an example image to…
Keyboard Shortcuts
Getting Started » Keyboard Shortcuts
*On Mac systems, use CMD instead of CTRL. All Windows Zoom CTRL+D or Scroll Wheel Pan CTRL+F or Scroll Click and Drag Toggle Zoom/Pan CTRL Measure (if appl.) CTRL+M Recipe Step Preview…
v3.0.0 Release Notes
Release Notes » v3.0.0 Release Notes
Major New Features Deep Learning The most significant new technology to come to MIPAR yet. Teach MIPAR to detect even the most complex features simply by tracing. Models are trained in the new Deep Learning Trainer. Trained models can be applied to images as…
v4.0.0 Release Notes
Release Notes » v4.0.0 Release Notes
New Features Curve Fitting Added curve fitting to the Color by Measure, Local Measurements and Histogram of Measurements windows. Users are now able to add normal, log normal and bimodal fits to their data, as well as display fit parameters. These are…
Reconstruction
3D Toolbox » Reconstruction
Tutorial Shows the workflow for creating, processing, visualizing, and measure a 3D Reconstruction. Downloads You may download the below assets to use as learning tools and follow this tutorial. ⇩ Raw Dataset ⇩ Calibration Data ⇩ Segmentation…
v4.1.0 Release Notes
Release Notes » v4.1.0 Release Notes
New Features Load Multiple Images into Image Processor Image Processor can now open multiple images to combine into channels. Use File > Open Images to Channels. Batch Process Multichannel Data Using Alternative Data Structure Batch Processor can now…
v3.1.0 Release Notes
Release Notes » v3.1.0 Release Notes
New Features Copy & Paste It’s finally here. Now you can copy and paste an unlimited number of Recipe steps. To copy: click and drag, Shift-click, or Ctrl-click to select multiple steps and right-click > “Copy”, or “Ctrl+C”…
Intensity Mean
3D Toolbox » Measurements » Intensity Mean
3D Measurements > Intensity Mean Measures the average grayscale intensity within selection.
Intensity Sum
3D Toolbox » Measurements » Intensity Sum
3D Measurements > Intensity Sum Measures the total of grayscale intensity within selection.
Count
3D Toolbox » Measurements » Count
3D Measurements > Count Reports how many selected features are present in the reconstruction.
Surface Area
3D Toolbox » Measurements » Surface Area
3D Measurements > Surface Area Measures the total surface area of the selected features.
Volume
3D Toolbox » Measurements » Volume
3D Measurements > Volume Measures the total volume of selected pixels in the reconstruction.
Intensity StdDev
3D Toolbox » Measurements » Intensity StdDev
h.3 3D Measurements > Intensity StdDev Measures the standard deviation of grayscale intensity within selection.
Number Density
3D Toolbox » Measurements » Number Density
3D Measurements > Number Density Number Density measures the number of features per unit volume, where the total volume is specified in the ‘Relative To’ window.
Surface Area Fraction
3D Toolbox » Measurements » Surface Area Fraction
h.3 3D Measurements > Surface Area Fraction Surface Area Fraction measures the surface area of all the selected features in the active layer and divides it by the surface area of the layer specified in the ‘Relative To’ window.
Volume Fraction
3D Toolbox » Measurements » Volume Fraction
3D Measurements > Volume Fraction Measures the volume fraction of the selected pixels in the reconstruction. Counts all selected pixels in the active layers and divides it by the number of pixels in the layer specified in the “Relative To” window.…
Visualization
3D Toolbox » Visualization
MIPAR MIPAR provides basic tools for visualizing your 3D Reconstruction with tools like volume slicing, surface rendering, and simple animation. Avizo Avizo is the leading high-performance 3D visualization and analysis software for scientific and industrial data. We…
Slice-by-Slice Measurements
3D Toolbox » Measurements » Slice-by-Slice Measurements
Measurements > Slice-by-Slice Measurements Slice-by-Slice Measurements allows a variety of measurements to be made from each feature in each X-Y slice in the reconstruction. The 3D feature labeling is retained throughout the slices. Details of available measurements…
Tracing in Image Processor
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Tracing » Tracing in Image Processor
This example shows a Recipe-assisted approach to tracing features in the Image Processor. This approach is most useful for tracing grain boundaries, or other similar features. Load Image and Recipe ⇩ Download “trace-grains” recipe. This can be used as a…
POST Method
REST API » POST Method
There are two commands that can be sent to the REST API using a POST call: process and activate Start the MIPAR REST API Docker image With docker hub running, execute the command docker run -it -p The can be set by the user, for example 8000:8000 and the is…
Surface Measurements
3D Toolbox » Measurements » Surface Measurements
3D Measurements > Surface Measurements Surface Measurements allow you to make measurements from the currently rendered surface(s). *Surface measurements can take some time depending on the resolution and feature density of your rendered surface(s). It is recommended…
Feature Measurements
3D Toolbox » Measurements » Feature Measurements
3D Measurements > Feature Measurements Feature Measurements allows a variety of measurements to be made from each feature in the reconstruction or Layer. 1. Size Volume: Volume of each feature. Volume Fraction: Volume fraction occupied by each feature…
Manage Layers
Image Processor » Functions » View » Manage Layers
View > Manage Layers While Layers are most conveniently set, edited, and removed from the controls directly in the Image Processor, this window allows more control over Layer positioning. It also provides a comprehensive management center for your Layers. Layers are…
v4.3.0 Release Notes
Release Notes » v4.3.0 Release Notes
New Features Custom Measurements MIPAR now supports user defined measurements using formulas and mapping. Define new measurements using algebraic expressions, using existing measurements and other custom measurements as arguments. Map any measurement output to…
v4.2.1 Release Notes
Release Notes » v4.2.1 Release Notes
Improvements Flatten background can now accept an empty value. Bug Fixes Improved MIPAR error handling when loading a broken recipe. Improved Report Generator handling of vector elements in the current panel. Scale factor stays accurate after the last…
v3.1.2 Release Notes
Release Notes » v3.1.2 Release Notes
Bug Fixes Fixed bug where training settings panel in DLT could not be visible Fixed bug where “Remove Chapter” option in IP could not enable Fixed bug with “Undo” in PP and DLT Improvements Progress indicator now appears in 3DTB…
v3.4.4 Release Notes
Release Notes » v3.4.4 Release Notes
Improvements Added preference to normalize images before scaling to 8-bit. Preference is on by default and will continue normalizing 16-bit and 32-bit images based on their min and max when scaling to 8-bit. With preference off, 16-bit and 32-bit images will not…
Intercepts
3D Toolbox » Measurements » Intercepts
3D Measurements > Intercepts Random Lines Measures metrics such as mean intercept by drawing a specified number of random lines through the features in the reconstruction. 1. Number of Lines Number of lines to draw 2. Noise Removal Method for removing small…
Histogram of Measurements
Image Processor » Functions » Tools » Histogram of Measurements
Tools > Histogram of Measurements Plots a histogram from a .CSV or .TXT file of previously-made measurements. These files can be output from tools such as Measure Features, Color By Measurements, and Local Measurements. 1. Load To begin, load previously…
v4.2.2 Release Notes
Release Notes » v4.2.2 Release Notes
Improvements Added dedicated Path Length image and feature measurements Added ability to measure the exact floating-point Euclidean distance map as a Feature Image Intensity measurement Feature Measurements > Intercepts options have been changed from…
v3.3.0 Release Notes
Release Notes » v3.3.0 Release Notes
New Features Express Licenses Express Licenses are now available. These “runner licenses” are available at reduced rates and only allow recipe running (not building). Express Licenses provide all other Base License functionality. They are an…
Reject Features
Image Processor » Functions » Clean-Up » Reject Features
Clean-up > Reject Features Removes objects or fills holes based on their selected parameters being above or below a specified threshold. Parameter options include area, eccentricity, convex area/area ratio, and many more. Neighborhood conditionals are also optional,…
v3.4.0 Release Notes
Release Notes » v3.4.0 Release Notes
New Features Local Measurements in Recipe Add local measurements as a step in the recipe! They can be displayed with a simple click after recipe loading and summary stats (e.g., mean, min, max, etc.) of the local measurement will appear in the global…