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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…
Layout
Live » Layout
Access to MIPAR Live is gained through 1. the Recipe/Live Mode toggle. MIPAR Live MIPAR Live is laid out in three main sections, from right to left: Camera Controls, Live Image Preview, and Captured Image. Generally, a workflow proceeds from right to left as: 2.…
Layout
Image Processor » Layout
Below is labeled screenshot of the Image Processor which reveals the layout of and purpose behind each user interface element. *See Keyboard Shortcuts for shortcuts relevant to the Image Processor.
Layout
Batch Processor » Layout
Below is labeled screenshot of the Batch Processor which reveals the layout of and purpose behind each user interface element.
Layout
Real-Time Processor » Layout
Below is labeled screenshot of the Real-Time Processor which reveals the layout of and purpose behind each user interface element.
Layout
Report Generator » Layout
Report Types Available report types are as follows: Report Type Generated From Single Image Global Measurements table in Image Processor Single Image Feature Color by Measurements Single Image Local Local…
Measurement Layout
Session Processor / AI Session Processor » Measurements (formerly Post Processor) » Measurement Layout
Measurement Panel Layout Image Add global measurements, for example; total layer area, layer feature count, layer area fraction. Feature Add feature measurements, for example; area per feature, roundness per feature, nearest neighbor distance per feature. View…
General Layout
Session Processor / AI Session Processor » General Layout
Below is labeled screenshot of the Post Processor which reveals the layout of and purpose behind each user interface element. Measurements Layout AI Layout *See the Keyboard Shortcuts page for shortcuts relevant to the Post Processor.
AI Layout
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » AI Layout
Below is labeled screenshot of the AI Session Trainer which reveals the layout of and purpose behind each user interface element. Layout Train New Train new deep learning model using the reference and BW images and the Training Settings Update Model Update deep…
v3.2.4 Release Notes
Release Notes » v3.2.4 Release Notes
Bug Fixes Fixed bug with deleting some steps which depend on others Fixed bug where layers could all become temporarily identical when making “Outline” edits in PP and DLT Fixed bug where feature measurement stats CSV files were not properly comma…
v3.3.3 Release Notes
Release Notes » v3.3.3 Release Notes
Bug Fixes Fixed bug where feature measurements in PP could in some cases be formatted with incorrect units Fixed bug where scale factor would not display correctly in PP when reading a Bio-Formats image with embedded scale factor Fixed bug where mouse movement…
Find Edges
Image Processor » Functions » Segmentation » Find Edges
Segmentation > Find Edges Sets edge pixels as empty using the specified edge finding algorithm [1-3]. 1. Type The edge finding algorithm used Sobel: Detect edges using the Sobel algorithm Prewitt: Detect edges using the Prewitt algorithm Roberts:…
Find Facial Features
Image Processor » Functions » Segmentation » Advanced » Find Facial Features
Segmentation > Advanced > Find Facial Features Finds facial features in the Current Image such as frontal faces, profile faces, eyes, nose, mouth, and others. 1. Feature Sets type of facial feature to detect Face Frontal: Detects front-facing faces using…
*Active Contour
Image Processor » Functions » Segmentation » *Active Contour
Segmentation > *Active Contour Requires B/W Companion Image Uses active contouring [1,2] to set the boundaries of each feature in the Companion Image based on the Current Image. Active contouring grows or shrinks features to “snap” them to locally…
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…
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…
v3.3.2 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.…
*Grayscale Reconstruction
Image Processor » Functions » Pre-Processing » *Grayscale Reconstruction
Pre-Processing > *Grayscale Reconstruction Requires B/W Companion Image Changes grayscale pixel values based on features in the Companion Image. Available modes are morphological reconstruction, impose minima (ensures that minima in the grayscale image only occur…
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”…
v3.0.1 Release Notes
Release Notes » v3.0.1 Release Notes
Bug Fixes Deep Learning Training Fixed an issue where some deep learning models would not train based on their layer names. Fixed an issue where some deep learning models would not train from a Session output from a batch process. Portable Session Saving …
Find Circles
Image Processor » Functions » Segmentation » Find Circles
Segmentation > Find Circles Finds circles in the Current Image using an algorithm based on searching within the image’s Hough transform. This function can take some time to complete depending on the size of and number of circles in the image. 1. Method Sets…
*Mutual Information
Image Processor » Functions » Measurements » *Mutual Information
Measurements > *Mutual Information Requires Companion Image Measures the normalized and classical (absolute) amount of mutual information [1,2] between the Current and Companion images. The normalized value is a measure of image similarity that is well-suited for…
Color Cluster
Image Processor » Functions » Color » Color Cluster
Color > Color Cluster Assigns each pixel from the color Opened Image to one of the specified classes using k-means clustering [1-4]. This can be a powerful and objective way of segmenting color images. Works well for color images with 2 or more feature types of…
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…
Find Text
Image Processor » Functions » Segmentation » Advanced » Find Text
Segmentation > Advanced > Find Text Finds text in the Current Image using optical character recognition (OCR) [1] and places boxes around each detected word. *See the “Text” item under “Based on Companion” in Feature Measurements for…
Highlight Lines
Image Processor » Functions » Pre-Processing » Highlight Lines
Pre-Processing > Highlight Lines Uses the Frangi filter [1] to highlight linear-type features in the image. Combine with a threshold afterwards to select certain linear-type features. 1. Type Dark: Highlight dark linear-type features Bright: Highlight…
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…
Watershed
Image Processor » Functions » Segmentation » Watershed
Segmentation > Watershed Segments the Current Image by first interpreting its grayscale values as topography (ie, basins within level ground). A rainfall simulation is then run such that areas of similar intensity are separated from others, where their basins fill…
Smart Cluster
Image Processor » Functions » Pre-Processing » Smart Cluster
Segmentation > Smart Cluster Assigns each pixel to one of the specified classes using k-means clustering [1-4]. This can be a powerful and objective way of segmenting images. Works especially well for images with 3 or more feature types of interest, where different…
Non-Local Means
Image Processor » Functions » Pre-Processing » Non-Local Means
Pre-Processing > Non-Local Means Reduces image noise using an advanced filtering algorithm [1]. Each pixel’‘s local window is compared to windows around it. The windows’ center pixels are averaged together with weights depending on the variations…
Superpixels
Image Processor » Functions » Pre-Processing » Superpixels
Segmentation > Superpixels Groups pixels into regions with similar values. This can be a helpful processing step prior to other segmentation or feature-finding steps. Uses the simple linear iterative clustering (SLIC) algorithm [1,2]. 1. Type Statistic to use to…
Basic Threshold
Image Processor » Functions » Segmentation » Basic Threshold
Segmentation > Basic Threshold Selects pixels based on whether they are below or above a certain pixel value. “Auto” determines this threshold value using Otsu’s method, which chooses the value which minimizes the average grayscale variance of the…
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…
Report Generator
Report Generator
Requires Report Extension The Report Generator is used to export MIPAR results into a Microsoft Office Word or PDF document. Topics System Requirements Layout Templates
Session Processor / AI Session Processor
Session Processor / AI Session Processor
Application Description The Session Processor and AI Session Processor is used to review Batch Process Sessions, generate measurements on a data set and train new Deep Learning Models. Topics Layout Measurements AI Training
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…
Batch Processor
Batch Processor
The Batch Processor is used for batch applying a Recipe to multiple images. A batch process will save the last Recipe step (or each Layer step) for each image, along with a spreadsheet of any global or feature measurements that were set in the Recipe.…
Measurements (formerly Post Processor)
Session Processor / AI Session Processor » Measurements (formerly Post Processor)
The Session Processor is used for reviewing the results of a batch or real-time process. All saved processed images are loaded and overlaid/outlined, etc. on their respective references. The user can flip through each processed result to assess accuracy. Manual edits…
Auto Segmentation
Image Processor » Functions » Segmentation » Auto Segmentation
Segmentation > Auto Segmentation May use up to two B/W memory images Uses Smart Find™, geodesic distance, or marker-based watershed segmentation to auto-identify features based on two seed images. One seed image roughly identifies features and the other the…
*Local Threshold
Image Processor » Functions » Segmentation » *Local Threshold
Segmentation > *Local Threshold Requires B/W Companion Image Selects pixels if they meet the specified criteria relative to each feature in the Companion Image. “Auto Threshold” mode calculates the Otsu-based optimum threshold for each feature.…
Snap Tool
Spotlight ✧˙₊ » Snap Tool
Snap is a new intelligent drawing tool powered by Spotlight. Available in Manual Edit and Session Processor, it lives alongside the other manual drawing tools. Layout 1. Activate Click to activate Snap. 2. Performance Mode Fast = lightweight model Accurate =…
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…
Live
Live
MIPAR Live is an extension that allows MIPAR to connect directly to a supported camera and capture images to analyze. It provides a direct path from image capture to analysis, without having to switch software or load image files into MIPAR. Topics Supported…
Image Processor
Image Processor
The Image Processor is the most commonly used app. It is used for building and editing Recipes, as well as applying Recipes to single images. Recipes are sequences of image processing steps, in the right order and with the right settings, which work to identify…
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…
AI (formerly Deep Learning Trainer)
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer)
Requires Deep Learning Extension The Deep Learning Trainer is used to train deep learning models, which are capable of automating some of the most challenging feature detection problems across many applications. Below is a short video demonstrating the use of the…
Preferences
Getting Started » Preferences
Layout 1. MIPAR Open Directory Default folder for opening and image or recipe on MIPAR launch. 2. Calibration and Measurements Units Calibration units are used to display the scale bar and are used as default during recipe calibration. Measurement units are used…
Measurements
Image Processor » Functions » Measurements
Layout 1. Active measurement 2. Show/Hide Measurements Panel 3. Run active measurement on active Recipe step or shown Layers 4. Edit active measurement settings 5. Edit which Layers the active measurement is executed on 6. Generate measurements report for all…
Optimization
Image Processor » Optimization
This interface allows you to setup and start recipe step (process) optimization (i.e., auto-setting determination). After selecting optimization parameters, you will be asked to enter a range for some of the process’ parameters. This will start a loop which will…
Spotlight Tool
Spotlight ✧˙₊ » Spotlight Tool
The Spotlight recipe step works like any other MIPAR recipe step. It’s applied on recipe load and interacts with the rest of the recipe like a detection step. Users have full access to the rest of the MIPAR toolkit which enables detection filtering, clean up and…
Training
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Training
Once features are traced, a deep learning model can be trained. This example shows how to train a deep learning model and assumes tracing has been completed as shown in either of the tracing examples. Downloads You may download the sample session file and reference…
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,…