Applications

Table of Contents

Basic Workflows

Creating a recipe
Executing a recipe

GPA Explorer

Data Integrity Report

Segment.ai
Segment Objects.ai
Convert.ai
Enhance.ai

Continue Training

NIS.ai Explorer

Integration in General Analysis 3 (GA3)

Segment.ai Example

3D Measurement

Bio Analysis Modules

Analysis Explorer

Analysis Explorer Basics
Usage
Managing Recipes
Batch Analysis Options

Cell Count Analysis

Cell Motility

Cell Proliferation

Wound Healing

General Analysis

Introduction to General Analysis
Graphical user interface
How To Set General Analysis
General Analysis in NIS-Elements - Model Use Case
General Analysis in JOBS Module - Appended Point Set Use Case
General Analysis in JOBS Module - Replaced Point Set Use Case

Image Intensity Analysis

Live/Dead Analysis

Sperm Motility

New Database
New Connection
Database Tables
User Permissions
Database Backup
Database View within Organizer
Creating Reports from Database

Deconvolution

Introduction to Deconvolution

Choosing the Deconvolution Method

Landweber Deconvolution
Richardson-Lucy Deconvolution
Blind Deconvolution
Fast Deconvolution
Resources

Determining the Point Spread Function (PSF)

Proper Sampling

Widefield Sampling
Confocal Sampling

Dialog Settings

Automatic Deconvolution
3D Deconvolution
2D Deconvolution
Live De-Blur Setup

Running Deconvolution

Extended Depth of Focus

EDF Step by Step
Edit Area in the Focused Image
Real Time EDF
Real Time EDF Manually (without motorized Z)

Filter Particle Analysis

Introduction to Filters

Analysis Overview
Filters Plugin Window Appearance

Basic Workflows

Operational Precautions
Filter Scanning
Defining Detection
Automatic particle measurement
Displaying Results
Creating Report

Advanced Functions

System settings
Advanced Scanning
Autofocus during scanning
Advanced particle detection
Advanced Measurement Options
Manual Editing of Particles
Size Classes Definition
Creating a Report Template

Introduction to FRET

Capturing FRET Image, FRET Calibration

Hardware Setup
FRET Calibration
FRET Method

Creating FRET Image

Creating FRET View

[Ca ²⁺] Ion Concentration Measurement

FRET Example

Ratio Experiment, Calcium Calibration

Setting up Optical configurations
Configuring 6D Dialog
Setting up ROIs on Preview Image
Time Measurements Set Up
Capturing the Data Set
Calcium Calibration
Export Data

Custom Equation

Copy image
Inverted image
Gamma image
Difference image
Increasing intensity image

General Analysis 3

Introduction

Changes from 5.40

Basic Control

Toolbars and Menus
Functions, groups and sections

The NEMO Dots Assembly: Single-Particle Tracking and Analysis
Sholl Analysis
Spot Location
Tracking cells moving between chambers

Examples (version 5.42)

Mouse embryo detection analysis
Capturing embryos using rotated confocal scan area
Narrowing a Z-Stack
Custom shading correction on a wellplate
Stimulating objects (cells) based on their feature (intensity)
Histogram / Classification
Topography analysis
Proper cell detection
Renumbering objects
Inside and border of cells
Parent-child relation
Pairwise object analysis
Tracking
Cell cycle monitoring
Rare events - metaphase
Heartbeat analysis
Skipping empty cells
Manual region list definition

Image Processing
Image Operations
ND Processing & Conversions
Segmentation
Binary processing
Binary operations
Measurement
Data management
Results & Graphs
Sources & Reference
NIS.ai
Tracking
Hidden Nodes (created in NIS-Elements 5.4x)

Introduction to HCA

Jobs Explorer and Jobs Toolbar

Running a HCA job, viewing results

HCA Analysis

HDR Options
HDR module background

Illumination Sequence

User Interface

Creating illumination patterns

Creating Piezo Z Stack and Z Offset patterns

Piezo Z Stack
Piezo Z Offset

Creating stimulation patterns for Other Devices

Camera Timing Examples

Usage Examples

Supported cameras and illumination devices

Supported cameras
Supported illumination devices

JOBS and HCA

Introduction to the JOBS Module

Main Concept
Introduction to Jobs Explorer
Jobs Explorer Options
Job Definition Window
Job Definition Window Tools
Jobs Toolbar

Basic Job Rules

Creating a Job

New Job from Template
New Blank Job
Using Job Definition Wizard
Defining Samples
Defining Capture
Defining Loops
Defining Parameters

Merging Different Acquisition Types

Simple Acquisition Tasks Inside a Parent Loop
Merging Matching Z-Stacks
(Not) Merging Z-Stacks Different for Each Point
Multi-point inside Multi-Point Loop

Running a Job, Viewing Results and Graphs

Job Execution Progress window
Result View
Graph View
Context menu on a job
Context menu on a job run

GA3 After Acquisition

Labels and Metadata

Labeling/Quantities window
Defining and Setting Labels
Defining and Setting Metadata
Labels and Metadata in Result View
Importing predefined presets from spreadsheet applications
Labeling during runtime

Advanced Topics

Job Database
SMTP Configuration for Sending Email/SMS Messages
Advanced Files Import

Analysis Use Cases
Using Conditions
Using Expressions
Using Questions
Using Time Lapse
Creating PFS Surface

Well Plates
Sample Holder
Time Series
Stage XY Points
Large Images
Z-Stack
ROIs
Autofocus + Focus Surface
PFS
Acquisition
Stimulation
Optical Configurations
Conditions
System
Analysis
GA3 Processing
Device Control

Layer Thickness Measurement

Basic Layer Measurement
Calo Test

Measurement Sequencer

Introduction

Basic Workflow

Measurement Sequencer - Definition

Measurement Sequencer - Run

Measurement Explorer

Report Editing

Excel Template

Metalo - Cast Iron Analysis

Features of the Cast Iron Analysis Module:

Single Image Measurement

Sequential Measurement

Detection Panel
Measurement Panel
Left Tool Bar
Data Panel

Metalo - Grain Size Analysis

Introduction

Features of the Grain Size Analysis Module
Supported Industrial Standards
Methods
Measurement Modes
Copyright Information

User Interface

Application Workspace
Detection Panel
Measurement Panel
Measurement Mask
Display Modes
Data Panel

Direct Mode

Wizard Mode

Basic Workflow
Automatic Capture
Manual Capture

Planimetric Method

Planimetric Method Settings
Overlay Transparency
Manual Corrections Before Measurement
Application of the Standards in the Planimetric Method

Intercept Methods

Manual Corrections Before Measurement

Comparative Method

Introduction
Physical Zoom
Comparison Charts Workflow
Tools of the Comparison Window
How to Create Your Own Grain Size Comparison Charts

Data output and Reports

Export to Report Template
Export Options

Left Tool Bar
Detection Panel
Measurement Panel
Data Panel
Grain Size Wizard - Start
Grain Size Wizard - Select Detection Preset
Grain Size Wizard - Select Measurement Preset
Sequential Measurement

N-STORM Acquisition and Analysis

Control Windows

Molecule Options
Molecule Analysis
Reference

N-STORM Z-Calibration (Agilent and LU4)

Overview
Acquisition of Z-Calibrations with Agilent laser box
Acquisition of Z-Calibrations with LU4 laser box
3D Calibration
Generating a 2D Warp
Error messages during 3D calibrations
N-STORM calibration commonly asked questions

Triggered Acquisition

Introduction to Triggered Acquisition

What You Need to Run Triggered Acquisition

Master Camera Wiring
Wavelength Switcher Wiring
Piezo Z Wiring
Wiring Overview
Wiring Examples

Settings in NIS-Elements

Installation of a DAQ board
Camera Settings
Device Manager Settings
Acquisition Settings
Creating Optical Configurations for Multi-channel Triggered Acquisition
Using speed up with NIDAQ board

Object Classifier

Defining Classes

Smart Experiment

Introduction
Selecting and Running an Assay
Browsing Results
Assay Settings
User Management

Introduction to Tracking

Tracking Prerequisites

ROI Tracking Step by Step

Binary Tracking Step by Step

Visualization

Measurement of Tracking Features

Graph Properties

Tracking Options

Algorithm Overview

Frame-to-frame object linking
Object Features
Track Processing

Tracking Output Calculation

Track Segments
Acceleration
Heading and Elevation
Line Length and Speed
Reference Line Length

Tracking - Advanced

Tracking options
Track processing
Graph, Data and Tracks tabs

Tracking 3D

Single Particle Tracking

Import Molecule List

Real Time Tracking Using XY Stage

Intra-Nuclear Single Particle Tracking (I-SPT)

Overview
NIS-Elements configuration
Image analysis
Recipes
Detection
Tracking
I-SPT Outputs
Advanced I-SPT
Advanced tracking
Statistics

Weld Measurement

Basic Workflow

Concrete Measurement