QI Tissue

▲ QiTissue

↳ Welcome to the QiTissue Help Pages

↳ Application Performance and QiCloud Integration

↳ User Interface

Download

What's New?

▲ Hardware Requirement Specifications

↳ Operating System

↳ CPU

↳ GPU

↳ RAM

↳ Storage

↳ Display

↳ External Display

▲ Videos

▲ Software Training Compilation

↳ Tutorial

▲ Project Browser

↳ Basic Project Browser Tutorial

▲ Basic Image Display

↳ Basic Image Display Tutorial

▲ Sequencer

↳ Basic Sequencer Tutorial

▲ Feature Table

↳ Basic Feature Table Tutorial

▲ Correlation Matrix

↳ Correlation Matrix Tutorial

▲ Workflow Editor

↳ Basic Workflow Editor Tutorial

▲ UMAP, t-SNE, and Clusters

↳ Basic UMAP, t-SNE, and Clusters Tutorial

▲ Scatter Plot and Gating

↳ Basic Gating Tutorial

▲ Segmentation

↳ Basic Segmentation Tutorial

▲ Feature Plot

↳ Basic Feature Plot Tutorial

▲ Getting Started

▲ Naming your Datasets

↳ What is Cyclic Immunofluorescence?

↳ File Naming Structure

↳ Create Your Custom Naming Scheme

▲ Using the Project Browser

↳ New and Cached Datasets

↳ What is Cache?

↳ Memory Management

▲ Key Folder Locations

↳ Application Support

↳ User Data Directory

↳ Image Cache Directory

↳ Shortcut to access hidden folders

▲ Image Display & Visualization Control: The Basics

↳ Image Contrast

↳ Adjust Image Curve

↳ Thresholding

↳ Export Display Settings

↳ Channel List

↳ Favorites

↳ Registration

↳ 3D View

▲ Workflow Layouts

↳ Processing Layout

↳ Visualization Layout

↳ Analysis Layout

▲ Feature Data

↳ Why Annotate?

↳ Segmentation

↳ Analyzing Feature Data

↳ Gating

▲ Documentation

▲ License Management

↳ Moving Your License to a New Computer

↳ Non-Networked Computers

▲ Project Browser

↳ Organizing Image Data

↳ Navigating Your Files

↳ View Scenes in a Grid

▲ Channel Adjustment

↳ Channel Right-Click Options

↳ Color Palette

↳ Channels List Icon Bar

↳ Color Scheme Presets

↳ Channel Grouping

↳ Contrast Options

↳ Quality Analysis

↳ Channel Favorites

↳ Channel Table

▲ Histogram

↳ Image Display Settings

↳ Adjusting the Curve

↳ Hightlight a Data Range

↳ Blink Effects

↳ Default Blink Effect

↳ Slow Fade Blink Effect

↳ Y-Axes

▲ View Navigator

▲ Registration

↳ Automatic Registration

↳ Manual Registration

↳ Registration Settings

↳ Check Registration Settings

▲ Segmentation

↳ Parameters for Nuclear Segmentation

↳ Fine-Tuning Your Parameters

↳ Segmentation Methods

↳ Measuring Cell and Image Features

↳ Segmenting Regions of Interest

↳ Importing Segmentation Masks

▲ Properties Panel

↳ Channel

↳ View

↳ Annotation

↳ Cellset

↳ Attributes

▲ Tools

↳ Drawing

↳ Gating

▲ Cell Selection Overlays

↳ Importing Cluster Files

↳ Cluster Import File Format

↳ Additional Syntax

▲ Feature Table

↳ Set a Data Source

↳ Find Cells In Your Image View

↳ Import/Export Feature Data

▲ Feature Plot

↳ Set a Data Source

↳ Plot Types

↳ Export a Plot

↳ Plot Favorites

↳ Apply t-SNE/UMAP and K-Means Clustering

▲ Extra Plots

↳ Graphing Signal Levels

↳ Graphing Feature Values

↳ Additional Graphing Options

▲ Sequencer

↳ Create a Scene

↳ Using the Timeline

↳ Playback Options

↳ Transitions

↳ Examples of Transitions

↳ Sequencer Favorites

↳ Export

▲ Workflow Editor

↳ Gating Nodes

↳ Merge Nodes

↳ Cluster Nodes

↳ Import Gating Positions and Cell Phenotype Definitions

↳ Future Reuseable Components

Correlation Matrix

Reference Browsers

Diagrams

▲ Advanced Features

↳ Advanced Registration using ASHLAR

↳ Controls-based Normalization

▲ Machine Learning Segmentation

↳ ML Segmentation - Cellpose and Stardist

↳ ML Segmentation - Deepcell (experimental)

FAQ

Here are some guides to, you guessed it, get started.

Please check back here often for updated documentation.

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