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Session Processor (formerly Post Processor)
Getting Started » Tutorials » Session Processor (formerly Post Processor)
Reviewing a 2D Batch Shows how to review and edit multiple images after they have been batch processed to segment features of interest. Generating Measurements Shows how to generate measurements from multiple images after they have been batch processed to segment…
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…
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
Image Processor
Getting Started » Tutorials » Image Processor
Detecting Creating a Recipe Describes the process of creating a segmentation recipe to identify features of interest in an image. Optimizing Steps Shows the procedures and applications for optimizing, or objectively determining, image processing…
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…
Batch Processor
Getting Started » Tutorials » Batch Processor
Running a Batch Shows how to setup and run a batch process to segment and measure features from a set images.
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.…
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…
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…
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…
Tracing in AI Session Processor
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Tracing » Tracing in AI Session Processor
Fully Manual This example shows a fully manual approach to tracing features directly in the AI Session Processor. Downloads You may download the sample reference images to use as learning tools and follow this example. ⇩ Reference Images Load References Begin…
AI Session Processor (formerly Deep Learning Trainer)
Getting Started » Tutorials » AI Session Processor (formerly Deep Learning Trainer)
Demo Video illustrating the use of the AI Session Processor Tracing Shows examples of tracing features of interest to develop training data. Training Shows example of training a deep learning model. Applying Shows example of applying a deep learning model to a…
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.
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…
v3.0.4 Release Notes
Release Notes » v3.0.4 Release Notes
Bug Fixes Fixed bug where MIPAR loads a color image as grayscale due to small thumbnail in second TIF page Fixed bug where error tone is given when entering a factor in Resize Image Fixed bug where table from “Ruler Tool” is not shown properly in…
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
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 …
Overview
Getting Started » Tutorials » Overview
Tour Take a tour of MIPAR’s powerful features and intuitive workflow. You’ll see examples of feature detection, batch processing, and measurements. Demo Watch a full demo of MIPAR’s operation including the Image Processor, Batch Processor,…
v3.3.1 Release Notes
Release Notes » v3.3.1 Release Notes
Bug Fixes [All Apps] Would not be properly informed of unsupported image formats when trying to open [Color by Measurements] Changing the format of feature ID labels would duplicate the labels [Deep Learning Trainer] Image would not display properly after edits…
v3.0.3 Release Notes
Release Notes » v3.0.3 Release Notes
Bug Fixes Manual Edit Fixed an issue where Manual Edit step failed to open during edit if “Labels” was the default viewing mode. Recipe Saving Fixed an issue where if you had a Recipe with only measurement steps you would not one prompted to…
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…
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…
v4.2.2 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…
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…
v3.4.3 Release Notes
Release Notes » v3.4.3 Release Notes
Bug Fixes Using Replace with Triangulation on a segmentation with one feature will no longer cause a recipe failure Generating a summary report out of the Post Processor will no longer produce an error Generating Rotating Intercepts measurement on an empty…
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 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…
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…
v3.2.2 Release Notes
Release Notes » v3.2.2 Release Notes
New Functions Replace With > Nearest Distance replaces each feature with a line between it and its nearest neighbor. Bug Fixes Fixed bug where inserting an Apply Model step below another doesn’t update the dependencies of later Call Output steps Fixed…
Calibrating The Scale
Image Processor » Calibrating The Scale
Embedded Image Scale Factors MIPAR can read embedded scale factors from over 150 file formats once the Bio-Formats plugin is in place. See the Supported Formats page for more information on setting up this plugin. If an image is opened which contains an embedded…
Batch Analysis
Live » Batch Analysis
To perform batch analysis of captured images, use either the Batch Processor or the Real-Time Processor. The Batch Processor is useful if you wish to perform the analysis once all the images have been captured. The Real-Time Processor is useful if you wish each image…
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…
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…
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…
The Session
Batch Processor » The Session
Sessions When running a MIPAR Batch, Real Time Process, building a data set in the Session Processor or AI Session Processor, MIPAR will organize the data into a session. In the Batch Processor and Real Time Processor MIPAR automatically collects the detected binary…
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,…
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…
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.
v4.3.1 Release Notes
Release Notes » v4.3.1 Release Notes
Improvements Added the ability to save the current view from the Image Processor into a recipe, so that the view is restored when the recipe is restored. Remembered settings include Simple Mode, showing or hiding measurements, overlay vs. outline and their…
v4.0.1 Release Notes
Release Notes » v4.0.1 Release Notes
Improvements Included new Report Generator templates with fields for curve fit outputs. You will be prompted to replace current templates on first launch of v4.0.1.0. Apply Model will no longer force a minimum size factor. Measure Feature tool added to Session…
Refreshing the Camera List
Live » Connecting a Camera » Refreshing the Camera List
The camera list is populated when the Image Processor is opened. To refresh the camera list, close and re-open the Image Processor. The camera list is also populated when the Camera Setup window is opened. Opening the Image Processor or the Camera Setup window while…
Starting MIPAR Live
Live » Starting MIPAR Live
MIPAR Live resides inside the Image Processor and is started simply by starting the Image Processor from the Launch Bar (1). When you have an active MIPAR Live license, the Image Processor opens in Live mode. To switch between Live and Recipe modes, use the Live /…
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…
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.
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…
Tracing
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Tracing
There are several approaches to tracing features to setup a deep learning training. Below are examples of three recommended approaches. Tracing can be done directly in the Deep Learning Trainer (fully manual, or semi-automated), in the Image Processor, or in an…
v4.1.1 Release Notes
Release Notes » v4.1.1 Release Notes
Bug Fixes Viewing mode stays in “Layers” after switching from Simple to Detail after loading recipe in Image Processor. Average neighbor distance is now properly reported for only 2 features. Fixed bug when loading out-of-date recipes that apply…
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…
Developing an Analysis Workflow
Checkpoint (beta) » Developing an Analysis Workflow
Required materials MIPAR Base + Report Generator Images to analyze Building the recipe 1. Using the standard images and the MIPAR Image Processor, develop a recipe to perform the desired analysis 2. Record any Preferences that may impact analysis: Measurement…
Notes, Flags, Interruptible, Custom Recipe Names
Image Processor » Notes, Flags, Interruptible, Custom Recipe Names
Notes Notes are comments that users may add to any Recipe step. These can be useful for reminding yourself, or indicating to others, the intent behind a step. They can also be helpful in indicating which settings should be adjusted in situations when the Recipe needs…
The Recipe
Image Processor » The Recipe
MIPAR’s unique technology is the Recipe. Like an engine of a car, you use the one that’s right for the job. Make them yourself, start with one from the 80+ built-in templates, or get one custom-designed for you. Recipes are built in the Image Processor,…
Spotlight ✧˙₊
Spotlight ✧˙₊
Spotlight enables the next generation of feature detection. It is a based-on groundbreaking generalized artificial intelligence, enabling software to “see” objects from simple to complex, even those it has not been trained on. The technology has been…
Applying
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Applying
Once a deep learning model is trained, it can be applied to a new image to automate feature detection. Effectively, application of a deep learning model results in a pre-processed version of the original image, where features of interest are “lit-up”…
Resize Image
Image Processor » Functions » Edit » Resize Image
Edit > Resize Image Resizes the image to the new dimensions, or by a size factor. 1. Dimensions Resize image to new dimensions X: Enter new X-dimension. Leave blank (if Y is not) to maintain aspect ratio. Y: Enter new Y-dimension. Leave blank (if X is…
Load Companion Image
Image Processor » Functions » Memory » Load Companion Image
Memory > Load Companion Image Loads in an image from a file as the Companion Image and as the Current Image. If the chosen image’s directory will hold a set of images to be paired with starting images in a batch process, then select check the “Load for…
Batch Pause and Resume
Batch Processor » Batch Pause and Resume
Resuming a batch It is possible to resume a batch process that has finished or been stopped, provided the session has not been edited in the Session Processor. To resume a batch, use the “Resume Session” button to load the session file (.ssn or…
Controlling Camera Settings
Live » Controlling Camera Settings
Camera settings are controlled in the right-most panel of the Image Processor, in the same location as the Recipe panel in Recipe Mode. Basic settings are exposed directly in this panel. Advanced settings are available through the Advanced Settings button at the…
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…
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 =…
Reviewing a Batch
Session Processor / AI Session Processor » Measurements (formerly Post Processor) » Reviewing a Batch
Tutorial Shows how to review and edit multiple images after they have been batch processed to segment features of interest. Manual Editing For a list of available manual editing tools and their descriptions, please click the links the below: Manual Editing…
Apply Model
Image Processor » Functions » Deep Learning » Apply Model
Deep Learning > Apply Model Applies a trained deep learning model to the selected image. Output can be a probability map of any of the trained layers, or a layer map. A probability map indicates each pixel’s likelihood to belong to that layer. A layer map…
Recipe Templates
Image Processor » Recipe Templates
MIPAR v4.2.0 brought pre-built recipes right into the Image Processor. Over 80 recipes are available to browse and try on either the included example images, or your own. They are called templates as they are intended to be strong starting points for many solutions.…
Updating
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Updating
Updating a deep learning model allows new classes to be added without retraining on the entire set that had been used up to that point. However, our testing has shown that an extensively trained and validated model is required for updating to work properly. Whether…
Connecting a Camera
Live » Connecting a Camera
The list of available cameras is populated when the Image Processor is opened. To connect to a camera, select it from the camera dropdown: Reselecting a camera from the dropdown will reset the connection to the camera. When a camera is selected, MIPAR will take…
Applying Recipes
Live » Applying Recipes
To apply a recipe to a captured image, the recipe can be preloaded in Live Mode, using the Load Recipe button (1) or menu option. This causes the recipe to be placed in the Preloaded Recipe dropdown (2): This pre-loading can be performed either before or after…
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…
Functions
Image Processor » Functions
This section provides details on all functions available in MIPAR’s Image Processor. Each function’s page contains the following information: Title Path Summary Screenshot (if applicable) Parameters (if applicable) References (if…
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…
*Register Image
Image Processor » Functions » Edit » *Register Image
Edit > *Register Image *Register Image Requires Companion Image Aligns the Current Image to the Companion Image using either a translation, rigid, similarity, affine, or free-form registration. 1. Registration Type Free-Form: Allows full non-rigid image…
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…
v4.2.1 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…
Color Deconvolution
Image Processor » Functions » Color » Color Deconvolution
Color > Color Deconvolution Function is always applied to the original color image. Color Deconvolution is used to separate a color image into channels (colors) that are not the basic red, blue and green channels. It is a powerful tool in pre-processing color…
Completing Signoff
Checkpoint (beta) » Typical Workflow » Completing Signoff
1. Log on to MIPAR Checkpoint as a user with Signoff permissions with the instructions here 2. Choose the project to view 3. Check-out the project in Read-Only mode using the “Check Out (Non-editable)” button 4. Click the “MIPAR” button 5.…
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…
Tracing in External Application
Session Processor / AI Session Processor » AI (formerly Deep Learning Trainer) » Tracing » Tracing in External Application
There are several applications available for manual image tracing on desktop and mobile operating systems. Below are just a few of the options for Windows and Mac platforms: Windows Mac Adobe Photoshop x x Gimp x …
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.…
Recipe Store
Getting Started » Recipe Store
Enter Recipe Store ›› What Is It? The Recipe Store is a fantastic resource for getting the most out of MIPAR. Find and download Recipes for all sorts of segmentation problems. You’ll learn fast and accelerate your work. How Does It Work? Browse the…
Performing Analysis
Checkpoint (beta) » Typical Workflow » Performing Analysis
Starting the application 1. Open the MIPAR Checkpoint application 2. If necessary, connect to the Server 3. Enter User Login Information Opening project (If your project doesn’t exist yet) 1. Click the Projects dropdown in the upper-left corner 2a. (If…
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…
Manual Edit
Image Processor » Functions » Segmentation » Manual Edit
Segmentation > Manual Edit Opens the Current Image in an editor which allows for manual edits to its segmentation. Here you can add missed features and remove artifacts. Also useful for manually defining a region of interest (ROI), which when set in a memory image,…
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…
Install and Activate
REST API » Install and Activate
Standard Image Install Docker is a prerequisite to install the REST API, you can download docker here: LINK MIPAR support team will request the workstation Windows Edition and Version to ensure the Docker Image is compatible Make sure Docker is running Run the…
System Requirements
Spotlight ✧˙₊ » System Requirements
Summary Windows only in beta NVIDIA GPU with at least 6GB VRAM Other hardware in-line with general system requirements Operating System Spotlight beta is only available on Windows. Supported versions are: Windows 11 Windows 10 Windows 7 SP 1 Windows Server…
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”…
Channel Operation
Image Processor » Functions » Color » Channel Operation
Color > Channel Operation Performs an arithmetic operation on the channels of the opened image. Only applies to color images (i.e. images with multiple channels). Download a recipe of example channel operations for your color image. An example color image may be…