EPFL–SV–PTBIOP INTERNAL COURSE 2015 QUANTITATIVE IMAGING AN EXPERIMENT INVOLVING IMAGING Biological Question Protocol Development Imaging Image Analysis EPFL–SV–PTBIOP Conclusion 2 IMAGE PROCESSING/ANALYSIS Image Processing Image in Image out Image Aquisition Image Analysis Image in Numbers out Image understanding spatial domain frequency domain IMAGE PROCESSING Enhance -ment Filtering Image display Image restoration Feature extraction complexity Brightness/Contrast Look up tables Gamma function Segmentation Particle Analysis 3D rendering Deconvolution Structured Illumination Fourier transformation QUANTIFICATION Number Size Pixel intensity independent! Shape QUANTIFICATION Transmission Fluorescence Concentration Absorption Concentration Brightness 𝐼𝑇 𝑇= 𝐼0 𝐹𝐼 = 2.303 ∙ 𝑐 ∙ 𝜖(𝜆) ∙ 𝑙 ∙ 𝐼0 Φ𝑓 𝐸 = − lg 𝑇 = 𝑐 ∙ 𝜖(𝜆) ∙ 𝑙 Strictly Valid only for low concentrations IMAGES ARE ARTEFACTS Two images of same object (sample) imaged with the same microscope/objective! Object Image of Object STAINING & DETECTION SCHEME AD converter Detector 𝑐𝐴 ~𝑝𝑖𝑥𝑒𝑙 𝑣𝑎𝑙𝑢𝑒 Iemm. Iexc. Fluorophores per Antibody (nF) Secondary Antibody (AB2) Primary Antibody (AB1) Antigen (A) DETECTION DEVICES Array detector Photons Point detector photoelectrons Pixel value CONFOCAL MICROSCOPE Dwell time: 50 µs Dwell time: 6 µs Dwell time: 1.6 µs Pixel intensity is NOT proportional to the number of collected photons !!! SUMMARY DETECTOR LINEARITY CCD camera • Linear over a large range EM CCD • EM-gain: exponential PMT • Gain: exponential • Data normalization against pixel dwell time GaAsP/Avalanche photodiodes • Photon counting mode EPFL–SV–PTBIOP SYSTEM CALIBRATION • System calibration is necessary for comparison between different images •Image with the same microscope settings if possible • Direct monitoring of excitation power is necessary for comparison of different systems •Check for absence of fluorophore saturation • Measuring system PSF is a good way to monitor the system performance • Calibration should be repeated regularly to monitor stability of the system BACKGROUND Condition 1 Condition 2 Difference Ratio Condition 1 Condition 2 Difference Ratio Signal Background Measured Value 200 20 220 100 20 120 100 2 100.0 1.8 Signal Background Measured Value 200 100 300 100 100 200 100 2 100.0 1.5 Sources of Background: Dark Image, cross-talk unspecific staining, autofluorescence,… IMAGE PROCESSING • Background subtraction • Flat field correction • Photobleaching correction • Correct sampling • Filtering /deconvolution BACKGROUND SUBTRACTION original background Leica AF6000 63 x/1.3 Imm objective background corrected • Useful especially in transmission mode • Removes of dust particles, spots from the image FLAT FIELD CORRECTION 100 x/1.3 Oil objective • Useful especially in fluorescence mode • Flat field can be measured with calibration slide • Subtract dark image before flat field correction FLAT FIELD CONFOCAL MICROSCOPE Zoom: 1.0 pixel value Zoom: 0.6 60000 60000 50000 50000 40000 40000 30000 30000 0 300 600 900 60000 50000 50000 40000 40000 30000 30000 0 300 600 900 0 300 600 900 Zoom: 4.0 pixel value Zoom: 2.0 60000 0 300 position 600 900 position PHOTOBLEACHING CORRECTION • Max bleaching: fixed sample - 50%, live sample - 20% • For strong bleaching SNR is different at the beginning and at the end of the series • Fluctuations of laser or lamp power are corrected similarly IMAGE PROCESSING SUMMARY • Flatfield correction and background subtraction are already necessary for analysis within single image • For quantitation use images with at least 12 bit grey values • Use full dynamic range of detector with offset and gain settings preventing clipping or saturation • Use correct image sampling with pixel size 2 to 3 times smaller than resolution • To remove noise use Gaussian or mean filter with kernel size close to the resolution of the system 19 BIT DEPTH Does the selected bit depth correspond to the number of measured photons/photoelectrons? Bit Depth Grayscale Levels Dynamic Range (Decibels) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 16 18 2 4 8 16 32 64 128 256 512 1,024 2,048 4,096 8,192 16,384 65,536 262,144 6 dB 12 dB 18 dB 24 dB 30 dB 36 dB 42 dB 48 dB 54 dB 60 dB 66 dB 72 dB 78 dB 84 dB 96 dB 108 dB 20 1,048,576 120 dB QUANTITATIVE IMAGING • Getting quantitative information about the specimen from the image • It is necessary to avoid subjective bias and to present the overall pattern of the data • Relative quantification – measure relative intensity • Absolute quantification – measure the number of photons • Thick specimens are difficult to quantify due to scattering and absorption • Important for the most of light microscopy methods which are intensity based (e.g. Colocalisation, FRET, linear unmixing) PROTEIN LOCALIZATION EPFL–SV–PTBIOP nucleus nucleolus nuclear envelope cytoplasm nucleus + cytoplasm mitochondria peroxisomes microtubules focal adhesions endoplasmic reticulum Golgi plasma membrane 10mm http://gfp-cdna.embl.de/index.html COLOCALIZATION TYPICAL EXAMPLE Vinculin Alexa568 EPFL–SV–PTBIOP Actin Alexa488 http://www.olympusconfocal.com/applications/colocalization.html Colocalization: The presence of two or more fluorophores on the same physical structure (in a cell). COLOCALIZATION INDICATORS Pearson coefficient 𝑷𝑪𝑪 = (𝑹𝒊 − 𝑹) × (𝑮𝒊 − 𝑮) (𝑹𝒊 − 𝑹)𝟐 × (𝑮𝒊 − 𝑮)𝟐 Overlap coefficient 𝒐𝒗𝒆𝒓𝒍𝒂𝒑 = 𝑹𝒊 × 𝑮𝒊 𝑹𝒊 𝟐 × 𝒌𝟏 = 𝑹𝒊 × 𝑮𝒊 𝑹𝒊 𝟐 ; 𝒌𝟐 = 𝑮𝒊 𝟐 𝑹𝒊 × 𝑮𝒊 𝑮𝒊 𝟐 𝑹𝒊 , 𝑮𝒊 : 𝒊𝒏𝒕𝒆𝒏𝒔𝒊𝒕𝒚 𝒐𝒇 𝒕𝒉𝒆 𝒑𝒊𝒙𝒆𝒍 𝒊 𝒊𝒏 𝒊𝒎𝒂𝒈𝒆 𝑹 𝒂𝒏𝒅 𝑮 𝒓𝒆𝒔𝒑𝒆𝒄𝒕𝒊𝒗𝒆𝒍𝒚 𝑹, 𝑮: 𝒂𝒗𝒆𝒓𝒂𝒈𝒆 𝒊𝒏𝒕𝒆𝒏𝒔𝒊𝒕𝒚 𝒐𝒇 𝒕𝒉𝒆 𝒊𝒎𝒂𝒈𝒆 𝑹 𝒂𝒏𝒅 𝑮 𝒓𝒆𝒔𝒑𝒆𝒄𝒕𝒊𝒗𝒆𝒍𝒚 CORRELATION Pearson’s Correlation Coefficient: 0.94 EPFL–SV–PTBIOP ANTICORRELATION Pearson’s Correlation Coefficient: -0.94 EPFL–SV–PTBIOP EXCLUSION Pearson’s Correlation Coefficient: -0.29 EPFL–SV–PTBIOP PARTIAL OVERLAP Pearson’s Correlation Coefficient: -0.016 EPFL–SV–PTBIOP BIG/SMALL EXCLUSION Pearson’s Correlation Coefficient: 0.19 EPFL–SV–PTBIOP BIG/SMALL COLOCALIZATION Pearson’s Correlation Coefficient: -0.047 EPFL–SV–PTBIOP PEARSON COEFFICIENT EPFL–SV–PTBIOP COLOCALIZATION EPFL–SV–PTBIOP • Two different molecules can never be at the same physical spot at the same time. • Colocalization seen in images is coming from the low-pass filtering of the image formation in light microscopy. • Colocalization is an artificial phenomenon and therefore always relative. COLOCALIZATION ANALYSIS Object based EPFL–SV–PTBIOP “Nearest-Neighbor distance” “Overlap” • • • Binarization by: top hat (image) = image – morphological opening (image) Objects of channel2 reduced to their center of mass Count of “Yellow Dot => percentage • • • same as “Overlap” Analysis objects of both channels reduced to their center of mass If 2 centers of mass in different channels are less then a defined distance (depending on the resolution limit of the objective). They are colocalized => percentage E. Lachmanovich, Journal of Microscopy, 2003 33 COLOCALIZATION ANALYSIS Intensity based EPFL–SV–PTBIOP Scatterplots - Fluorograms Each position on a fluorogram correspond to the pixels with the green and red corresponding components The color on the scatterplot corresponds to the frequency of this value in the image. DISPLAYING COLOCALIZATION EPFL–SV–PTBIOP • Consider color-blindness. • • Use Yellow/Blue or Green/Magenta Show the scatterplot at the same time! Green Channel Showing Overlaps Red Channel Color-blindness simulation (Dichromacy) Quiz: What’s the color of the colocalization? 35 DISPLAYING COLOCALIZATION EPFL–SV–PTBIOP The Scatterplot or 2D Histogram Green Channel The eyes (and brain) lie! Complement: Colocalized Pixel Map Red Channel Helps see correlation qualitatively, no bias, unlike color merge. Helps to see problems from imaging ANALYSIS: FLUOROGRAMS EPFL–SV–PTBIOP Why do we like Fluorograms? Saturated Noisy Saturated No correlation? Wrong Offset Wrong Offset Bleed through ANALYSIS EPFL–SV–PTBIOP “Intensity based” colocalization Quiz: Which scatterplot belongs to which image series? 1 2 3 4 Result: A3, B1, C4, D2 ANALYSIS: INTENSITY-BASED “Intensity based” colocalization THRESHOLDING from CONTROLS!! EPFL–SV–PTBIOP ANALYSIS: INTENSITY-BASED EPFL–SV–PTBIOP “Intensity based” colocalization Li’s Intensity Correlation Quotient (-0.5 to 0.5) Partial colocalization Mito-DsRed; ER-GFP The ICQ is based on the non-parametric sign-test analysis of the PDM values. and is equal to the ratio of the number of positive PDM values to the total number of pixel values. The ICQ values are distributed between 0.5 and +0.5 by subtracting 0.5 from this ratio. ICQ = 0: Random Staining -0.5 < ICQ < 0: Seggregated Staining PT-BIOP 2012: Colocalization 0 < ICQ < 0.5: Dependent Staining 40 ANALYSIS: AUTOTHRESHOLDING EPFL–SV–PTBIOP Subjective bias during threshold selection makes for poor reproducibility Suggested method: Iteratively find where the Pearson’s correlation below thresholds <= 0 PT-BIOP 2012: Colocalization 41 STATISTICAL TESTING EPFL–SV–PTBIOP Are your colocalization results better than random chance? Costes’s Method 10/35 Pixels Colocalize: Is that real or due to random chance? Statistical confidence P - Costes et al. 2004 Biophysical J. vol 86 p3993 PT-BIOP 2012: Colocalization 42 STATISTICAL TESTING EPFL–SV–PTBIOP Costes’ Method - Randomization Our result: 10 Not by chance 1. Randomize one image in PSFsized chunks 2. Measure correlation, overlap or other metric 3. Repeat 100 times or more. 4. How many randomized images have better or equal correlation than the original? • 9 10 Statistical confidence P - Costes et al. 2004 Biophysical J. vol 86 p3993 PT-BIOP 2012: Colocalization If >95% are worse: we can start believing our numbers. The p-value P = 0.50 = 50% (No) P = 0.95 = 95% (yes..) P = 1.00 = 100% (YES!) 43 STATISTICAL TESTING EPFL–SV–PTBIOP Costes’ Method – Example Virus entry to Calveolae T = 10 Min. • 32% of virus colocalized • • Costes P-value 0.00 0% chance it’s true T = 20 Min. • 39% of virus colocalized • • Daniel J. White – CBJ @ Max Planck PT-BIOP 2012: Colocalization Costes P-value 1.00 «100%» chance it’s true Without significance test, we wrongly assume virus is colocalised with caveolae at 10 min P.I. It is not! Only at 20 min is there signficant correlation. 44 THANK YOU! EPFL–SV–PTBIOP References https://ifn.mpicbg.de/wiki/ifn/images/f/fa/QuantitativeColocAnalysis-10-2011.pdf http://fiji.sc/wiki/index.php/Colocalization__hardware_setup_and_image_acquisition And The Monty Python! PT-BIOP 2012: Colocalization 45 COLOCALIZATION MUST READ http://pacific.mpicbg.de/wiki/index.php/Colocalization_Analysis Costes et al. Manders et al. Bolte & Cordelières EPFL–SV–PTBIOP
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