Pipelines Glossary
Pipelines Glossary
Pipelines
Automatic ROI drawing with segmentation
Create BLANK reference image for multiwell plate using median
Create background reference image(s) for multiwell plate using median of wells
Create ROI sized as the image
Local background subtraction with median filtering (rolling ball)
Show color composite image
Subtract background and stabilize
Subtract background of TILED images using 2DDFT: calibrated
Subtract background of TILED images using 2DDFT: non-calibrated
Cell Counting and Colocalization
Applications - Cell death
Count live, apoptotic or necrotic cells POS. CTRL. REFERENCE
Count live, apoptotic or necrotic cells with IMAGE background subtraction POS. CTRL. REFERENCE
Count live, apoptotic or necrotic cells with IMAGE background subtraction
Count live, apoptotic or necrotic cells
Fraction of cell death time lapse POS. CTRL. REFERENCE
Fraction of cell death time lapse
Applications - Cellular senescence and aggregates
Count cells with aggregates using nuclear and whole cell markers
Count cells with foci vs diffuse fluorescence
Count cellular foci with secondary cell segmentation
Count nuclear or cellular foci
Count senescent cells with SA-BGAL staining densitometry
Applications - Histometry
Count cells or nuclei categorized by a shape parameter in tiled images
Count DAB positive nuclei in HE stained sections
Applications - Whole well counting
Microplate whole well cell count (automatic well positioning, with positive control)
Seahorse well cell count with nuclear stain LOAD well ROI
Seahorse well cell count with nuclear stain SAVE well ROI
Seahorse well cell count with nuclear stain with marker (immunocytochemistry)
Seahorse well cell count with nuclear stain
Cells or Nuclei segmentation
Whole well cell count
Whole well nuclear count time lapse with image background subtraction
Whole well strip cell count
Intensity Measurements
Applications - Calcium
CFP-YFP FRET - Fura crossbleed correction, FRET and Fura Ratio Image Calculation NFM
CFP-YFP FRET - Fura crossbleed correction, FRET and Fura Ratio Image Calculation
Mitochondrial calcium measurement with highpass filtering
Applications - Histometry and Micro Densitomtery
Basic fluorescence histometry using nuclear marker (1-3 labels)
Fluorescence and absorbance histometry using nuclear and secondary whole cell segmentation (1-4 labels - advanced background options)
Fluorescence and absorbance histometry using nuclear marker (1-4 labels - advanced background options)
Fluorescence histometry using nuclear and secondary whole cell segmentation (1-4 labels)
Measure DAB staining intensity in nuclei in HE stained sections
Optical density of tissue section - create reference image for OD BLANK using median
Optical density of tissue section
Perinuclear optical density measurement (SDH activity)
Applications - Membrane Potential
Mitochondrial membrane potential assay - measurement of the apparent activity coefficient ratio - 1 - process
Mitochondrial membrane potential assay - measurement of the apparent activity coefficient ratio - 2 - plot
Mitochondrial membrane potential assay - measurement of spectral crossbleed
Mitochondrial membrane potential measurement (TMRM/FLIPR) for CONFOCAL microscopy - for groups of cells
Mitochondrial membrane potential assay (TMRM/FLIPR) for CONFOCAL microscopy
Mitochondrial membrane potential assay (TMRM/FLIPR) with masking dead cells - for groups of cells
Mitochondrial membrane potential assay (TMRM/FLIPR) with masking dead cells
Mitochondrial membrane potential assay (TMRM/FLIPR) with post-hoc absorbance classifier
Mitochondrial membrane potential assay (TMRM/FLIPR) with post-hoc ICC-based ROI drawing
Mitochondrial membrane potential assay (TMRM/FLIPR)
Plasma membrane potential and GFP intensity single-cell analysis using post-hoc seed image
Plasma membrane potential and intracellular calcium single-cell analysis
Plasma membrane potential single-cell analysis using post-hoc seed image
Plasma membrane potential single-cell analysis
Applications - Reactive Oxygen Species
DCFDA normalized rate in all cells of a whole view field
DHE rate of ethidium formation normalized to dihydroethidium
MitoSOX MitoTracker Deep Red Ratio End Point POS. CTRL. REFERENCE
MitoSOX:MitoTracker Deep Red Ratio End Point with Post-hoc ICC-based Gating
MitoSOX MitoTracker Deep Red Ratio End Point
MitoSOX to MitoTracker Deep Red rates 2 channels
MitoSOX to MitoTracker Deep Red rates 3 channels
FRET image (three channel)
Measure fluorescence ratio in single-cells using segmentation-based ROIs
Measure fluorescence ratio of whole view field with background masking
Measure fluorescence ratio with magic wand-based ROI drawing
Measure intensity of membranes
Measure intensity of whole view field with background masking
Measure intensities corresponding to segments
Measure intensities in single-cells in two channels with spectral unmixing and using post-hoc seed image for segmentation
Measure of intensities in single-cells in two channels with spectral unmixing
Measure intensities in single-cells using ROIs drawn by segmentation
Measure intensities using segmentation of another image
Measure intensities using segmentation of the same image
Prepare two-channel time lapse for intensity analysis with spectral unmixing and subtraction of inhomogeneous background
Prepare two-channel time lapse for intensity analysis
Morphological Measurements
Applications - Fat droplets
Create reference image for OD BLANK and FLUORESCENCE BG using median
HE brightfield fat droplet analysis
Oil-red-O Fat droplet analysis
Applications - Histometry
Morphometry of hematoxylin stained nuclei in brightfield sections
Neurite outgrowth assay - reference image setup
Neurite outgrowth assay
Applications - Physiology
Mitochondrial swelling assay by thinness ratio
Applications - Volume Fractionator
Mitochondria to cell volume fractionator - mask debris
Mitochondria to cell volume fractionator - recalculate volume fraction
Mitochondria:cell volume fractionator (basic - remove out of focus)
Mitochondria:cell volume fractionator (basic)
Mitochondria:cell volume fractionator (multiplexed)
Mitochondria:cell volume fractionator (original)
Mitochondria:cell volume fractionator (basic with hole filling)
Mitochondria:cell volume fractionator (basic with post-hoc staining and hole filling)
Mitochondria:cell volume fractionator (basic with post-hoc staining)
Measure MEAN shape parameters for cells or nuclei
Measure mitochondrial MEAN shape parameters
Measure mitochondrial shape parameters
Measure mitochondrial skeletal length
Measure MULTIPLE shape parameters of cells or nuclei in tiled images
Measure shape parameters for cells or nuclei
Segment mitochondria
Motion Measurements
Measure tracking parameters of cells in brightfield time lapses
Track segments with one intensity channel
Measure velocity of cells or nuclei using tracking
Snippets
Brightfield processing Hematoxylin+DAB
Conditional export with automatic file naming
Draw perimeter of segments
Function with multiple inputs and outputs
If clause
Optional local background subtraction
Organize multiple plots from the same image into columns
Parallel processing with detection of the number of channels present
Rescaling image intensity with reference image choice
Rescaling image intensity
Rolling median background subtraction
Using the param variable
Video and Image Export
Video or image export 1-4 channels with local background subtraction cropped, stabilized
Video or image export 1-4 channels with local background subtraction with fixed scaling
Video or image export 1-4 channels with local background subtraction
Description:
This list reflects the default contents of the Pipelines menu.
Pipelines Glossary
