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Cytoflow 1.3.1 documentation

  • User manual
  • Developer Manual
  • GitHub
  • User manual
  • Developer Manual
  • GitHub

Section Navigation

  • Tutorials
    • Tutorial: Quickstart
    • Tutorial: Dose-Response
    • Tutorial: Hierarchical Gating
    • Tutorial: Estimating Genome Size
    • Tutorial: Microbial Diversity
    • Tutorial: Yeast Multidimensional Induction Timecourse
    • Tutorial: Synthetic Gene Logic Network
    • Tutorial: Transcriptional Repressor Characterization
    • Tutorial: Machine Learning
    • Tutorial: Computational Cytometry
  • How-To Guides
    • HOWTO: Install Cytoflow
    • HOWTO: Import an experiment from a table
    • HOWTO: Compensate for bleedthrough
    • HOWTO: Use beads to correct for day-to-day variation
    • HOWTO: Use the TASBE workflow for calibrated flow cytometry
    • HOWTO: Export FCS files
    • HOWTO: Export plots
    • HOWTO: Use different gates for different subsets of data
    • HOWTO: Add error bars to a statistics plot
  • Users’ guides
    • Guide: Using facets to compare data sets
    • Guide: Using statistics to summarize data
    • Guide: Which measure of center should I use?
    • Guide: How can I understand the experiment structure?
  • Operation and View Gallery
    • Autofluorescence correction
    • Bead Calibration
    • Binning
    • Linear Bleedthrough Compensation
    • Categorical Gating
    • Channel statistic
    • Color Translation
    • Density Gate
    • FlowClean
    • FlowPeaks Clustering
    • Gaussian Mixture Model (1D)
    • Gaussian Mixture Model (2D)
    • Hierarchical Gating
    • Import Files
    • KMeans
    • Minimum Spanning Tree Gate
    • Multi-channel statistic
    • Principal Component Analysis
    • Polygon Gate
    • Quadrant Gate
    • Range Gate
    • 2D Range Gate
    • Ratio
    • Registration
    • Self-Organizing Map Clustering
    • TASBE Calibrated Flow Cytometry
    • Threshold Gate
    • t-Stochastic Neighbor Embedding
    • Transform statistic
    • Bar Chart
    • Density Plot
    • Export FCS
    • Histogram
    • 2D Histogram
    • 1D Kernel Density Estimate
    • 2D Kernel Density Estimate
    • Long Table
    • Matrix Chart
    • Minimum spanning tree plot
    • Parallel Coordinates Plot
    • Radviz Plot
    • Scatterplot
    • 1D Statistics Plot
    • 2D Statistics Plot
    • Table
    • Violin Plot
  • Screenshots of the Cytoflow GUI
  • Frequently Asked Questions
  • User manual
  • Operation and View Gallery

Operation and View Gallery#

Below is a gallery of Cytoflow’s operations and views. Each header will take you to the corresponding manual page.

Operations#

Gates#

Threshold Gate
Threshold Gate
Range Gate
Range Gate
Quad Gate
Quadrant Gate
Rectangle Gate
2D Range Gate
Polygon Gate
Polygon Gate
Gate Hierarchy
Hierarchical Gating
Gate Categories
Categorical Gating

Preprocessing#

Linear Bleedthrough Compensation
Linear Bleedthrough Compensation
FlowClean
FlowClean
Peak Registration
Registration
Autofluorescence Correction
Autofluorescence correction
Bead Calibration
Bead Calibration
Color Translation
Color Translation
TASBE
TASBE Calibrated Flow Cytometry

Clustering#

Binning
Binning
Density Gate
Density Gate
One Dimensional Gaussian Mixtures
Gaussian Mixture Model (1D)
Two Dimensional Gaussian Mixtures
Gaussian Mixture Model (2D)
K-Means Clustering
KMeans
FlowPeaks
FlowPeaks Clustering
Self-organizing maps (SOM)
Self-Organizing Map Clustering
Minimum Spanning Tree
Minimum Spanning Tree Gate

Dimensionality Reduction#

Principal Components Analysis (PCA)
Principal Component Analysis
t-Distributed Stochastic Neighborhood Embedding (tSNE)
t-Stochastic Neighbor Embedding

Statistics and Transforms#

Channel Statistic
Channel statistic
Multi-Channel Statistic
Multi-channel statistic
Transform Statistic
Transform statistic
Ratio
Ratio

Views#

One Dimensional#

Histogram
Histogram
One-dimensional KDE
1D Kernel Density Estimate
Violin Plot
Violin Plot

Two Dimensional#

Scatterplot
Scatterplot
Density Plot
Density Plot
Two-dimensional histogram
2D Histogram
Two-dimensional KDE
2D Kernel Density Estimate

Multi-Dimensional#

Parallel Coordinates Plot
Parallel Coordinates Plot
Radviz
Radviz Plot

Statistics#

Bar Chart
Bar Chart
1D Statistics Plot
1D Statistics Plot
2D Statistics Plot
2D Statistics Plot
Matrix View
Matrix Chart
Minimum Spanning Tree
Minimum spanning tree plot

Miscellaneous#

Table View
Table
Long Table View
Long Table
FCS Export
Export FCS

previous

Guide: How can I understand the experiment structure?

next

Autofluorescence correction

On this page
  • Operations
    • Gates
    • Preprocessing
    • Clustering
    • Dimensionality Reduction
    • Statistics and Transforms
  • Views
    • One Dimensional
    • Two Dimensional
    • Multi-Dimensional
    • Statistics
    • Miscellaneous

© Copyright Massachusetts Institute of Technology 2015-2018, Brian Teague 2018-2026.

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