Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs...
Transcript of Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs...
![Page 1: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/1.jpg)
COLOCALIZATION ANALYSIS
+ =
Center for Microscopy and Image Analysis
Urs Ziegler ([email protected]) Caroline Aemisegger ([email protected])
![Page 2: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/2.jpg)
ColocalizationThe presence of two or more structures on the same location.
Colocalization is always relative!The nearer the objects the higher the chance that they interact.
![Page 3: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/3.jpg)
Colocalization in fluorescence microscopy at subcellular level
Definition: The presence of two or more fluorochromes on the same physical structure in a cell.
Limitation in best case scenario: optical resolution of microscope (Light microscope: 200 x 200 x 400 nm)
Colocalization never measures interaction, itjust states that two dyes are close in a definedvolume.
www.olympusconfocal.com/applications/colocalization.html
![Page 4: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/4.jpg)
Guidelines for preparation and acquisition of samples for colocalization analysis
• Choice of fluorochromes: not too close, not too far (bleedthrough, chromatic aberration)
• Controls: for positive and negative colocalization, autofluorescence, single labelled controls
• Confocal; Widefield/ Deconvolution
• Appropriate objective (high numerical aperture (leads to small detection volume), highly corrected)
• Avoid bleedtrough/ crosstalk
• Minimize noise (Confocal: averaging/low speed; Widefield: camera, optimize exposure time)
• Dynamic range: use whole range, no saturation
• Proper sampling frequency (Nyquist sampling: about 3 pixels over resolution distance)
FITC/Cy3
![Page 5: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/5.jpg)
Analysis Tools
Visualization Quantification
RGB overlay
Imaris, ImageJ,Leica, Photoshop
Intensity based Object based
Correlation of the strength of linear relation between two channels.
Imaris, ImageJ Imaris, ImageJ
Structure identification anddetermination of overlap of objects.
![Page 6: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/6.jpg)
Colocalization visualizationgreen + red = yellow ?
Don`t trust your eyes in colocalization.Never overlay 3D projections.
Bolte et al., Journal of Microscopy 2006,Vol. 224, 213
![Page 7: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/7.jpg)
Analysis Tools
Visualization Quantification
RGB overlay
Imaris, ImageJ, Leica, Photoshop
Intensity based Object based
Correlation of the strength of linear relation between two channels.
Imaris, ImageJ Imaris, ImageJ
Structure identification anddetermination of overlap of objects.
![Page 8: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/8.jpg)
Intensity correlation based analysis
• The scatterplot/ 2D histogramm:
• The coefficients:
Pearson coefficient
Manders coefficients
Costes approach
Software: Imaris, ImageJ and others
![Page 9: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/9.jpg)
LIVE DEMOIntensity based analysis
Data sets : M.Walch, U.Ziegler et al., Uptake of Granulysin via Lipid Rafts Leads to Lysis of IntracellularListeria innocua.The Journal of Immunology, 2005,174:4220-4227.
![Page 10: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/10.jpg)
Walch et al, J. Immunol.,2005,174:4220
![Page 11: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/11.jpg)
The scatterplot
Overlay green/red
Good first visual estimate of colocalization. Information about image quality.
☺
Bolte et al., Journal of Microscopy 2006,Vol. 224, 213
Only qualitative correlation.
![Page 12: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/12.jpg)
Quiz: Which scatterplot belongs to which image series?
1 2
3 4
Result: A3, B1, C4, D2Bolte et al., Journal of Microscopy 2006,Vol. 224, 213
![Page 13: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/13.jpg)
Rr= 1: perfect colocalizationRr= 0: random localizationRr= -1: perfect exclusion
The Pearson Coefficient (PC): The Formula
![Page 14: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/14.jpg)
![Page 15: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/15.jpg)
Understanding the Pearson Coefficient
PC:-0.108 PC:0.169
PC:0.446 PC:0.446 PC:0.446 PC:0.228
The PC is not dependent on a constant background and on image brightness.☺The PC is not easy to interpret and affected by addition of non-colocalizing signals. No perspective of both channels.
![Page 16: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/16.jpg)
Manders coefficients
M1, M2 coefficient:
(Manders et al. , 1993)
Proportion of overlap of each channel with the other.
M = 1: perfect colocalizationM = 0: no colocalization
![Page 17: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/17.jpg)
Understanding the Manders coefficients
PC:-0.108 PC:0.169 PC:0.446
PC:0.446 PC:0.446 PC:0.228
☺
PC:0.425
M1:0.000 M2:0.000 M1:0.250 M2:0.250 M1:0.500 M2:0.500
M1:0.500 M2:0.500 M1:1.000 M2:0.163 M1:0.500 M2:0.286
The Manders coefficients are easier to interpret than the PC. They are not sensitive to the intensity of overlapping pixels.
They are sensitive to background. A threshold has to be set!
![Page 18: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/18.jpg)
The influence of noise on the Pearson and Manders Coefficients
PC:0.446 PC:0.437 PC:0.425
M1:0.500 M2:0.500
All these coefficients are influenced by noise.Minimize noise at acquisition and eventually deconvolveyour dataset prior to analysis.
Deconvolution improves colocalization analysis of multiple fluorochromes in 3D confocal data setsmore than filtering techniques. L. Landmann. Journal of Microscopy 208:2, 134 (2002).
PC:0.422 PC:0.398
M1:0.490 M2:0.260 M1:0.490 M2:0.180
![Page 19: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/19.jpg)
A statistical approach: Costes method*
(A) Estimation of automatic threshold
(B) Statistical significance:
Compares PC for no-randomised with randomized images and calculates significance.
*
![Page 20: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/20.jpg)
Costes method: Randomization
https://info.med.tu-dresden.de/MTZimaging/
17/40 pixels overlap.Significant or random?
If >95% of random images correlate worse than real image, we can trust the correlation coefficient.
![Page 21: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/21.jpg)
Summary Intensity based analysis tools
-sensitive to noise and background-threshold has to be set!
- independent on brightness of image- good indication of the contribution of each channel to the colocalization
M1,M2: proportion of one channel signal coincident with signal in other channel Values from 0 to 1.
Manderscoefficients
-long calculating time (3D)
-statistical approach-minimizes influence of noise
Automatic thresholding,Calculation of significance.
Costesapproach
Correlation of intensity distribution between channels.Values from -1 to 1.
Meaning
-sensitive to noise-only reliable for high correlation- not easy to interpret
-independent on brightness of image- not influenced by constant background
Pearson coefficient
☺
![Page 22: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/22.jpg)
Analysis Tools
Visualization Quantification
RGB overlay
Leica, Imaris,ImageJ, PS
Intensity correlation based Object based
Correlation of the strength of linear relation between two channels.
Imaris, ImageJ Imaris, ImageJ
Structure identification anddetermination of overlap of objects.
![Page 23: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/23.jpg)
Object based analysis
Less dependent on intensities. May be automated.
1. Segmentation: Object / background
2. Connexity analysis: definition of objects
3. Calculation of colocalized volume, area, centroids..
☺Objects need to be segmentable; not for diffuse labelling.
![Page 24: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/24.jpg)
Summary
• Imaging technique:No saturation No bleed throughminimize noise
• Preprocessing of images:Deconvolution, Smoothing (Gaussian or Median Filter)Background subtraction
• Analysis:Combine different methodsAnalyse multiple images
![Page 25: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/25.jpg)
Image J: JACoP Plugin
![Page 26: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/26.jpg)
Links
• Imaris colocalization tutorial:www.bitplane.com/go/web-training/training-archive
• JACoP :http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:jacop_2.0:just_another_colocalization_plugin:start
• General Colocalization tutorials: http://www.macbiophotonics.ca/PDF/MBF_colocalisation.pdfhttp://www.olympusconfocal.com/applications/colocalization.html
![Page 27: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/27.jpg)
Thank you for your attention!
+ =
www.zmb.uzh.ch
![Page 28: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/28.jpg)
![Page 29: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/29.jpg)
![Page 30: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/30.jpg)
![Page 31: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/31.jpg)
![Page 32: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/32.jpg)
![Page 33: Center for Microscopy and Image Analysis - USP · Center for Microscopy and Image Analysis Urs Ziegler (ziegler@zmb.uzh.ch) Caroline Aemisegger (Aemisegger@zmb.uzh.ch) Colocalization](https://reader034.fdocuments.us/reader034/viewer/2022050716/5e16b213155024526921166f/html5/thumbnails/33.jpg)