.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "generated\examples\liver\plot_tristan_volunteers.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_generated_examples_liver_plot_tristan_volunteers.py: ========================================================= Clinical - rifampicin induced inhibition (short protocol) ========================================================= This example illustrates the use of `~dcmri.AortaLiver` for joint fitting of aorta and liver signals to a whole-body model. The use case is provided by the liver work package of the `TRISTAN project `_ which develops imaging biomarkers for drug safety assessment. The data and analysis was first presented at the ISMRM in 2024 (Min et al 2024, manuscript in press). The data were acquired in the aorta and liver of 10 healthy volunteers with dynamic gadoxetate-enhanced MRI, before and after administration of a drug (rifampicin) which is known to inhibit liver function. The assessments were done on two separate visits at least 2 weeks apart. The research question was to what extent rifampicin inhibits gadoxetate uptake rate from the extracellular space into the liver hepatocytes (khe, mL/min/100mL) and excretion rate from hepatocytes to bile (kbh, mL/100mL/min). 2 of the volunteers only had the baseline assessment, the other 8 volunteers completed the full study. The results showed consistent and strong inhibition of khe (95%) and kbh (40%) by rifampicin. This implies that rifampicin poses a risk of drug-drug interactions (DDI), meaning it can cause another drug to circulate in the body for far longer than expected, potentially causing harm or raising a need for dose adjustment. **Note**: this example is different to the 2 scan example of the same study in that this uses only the first scan to fit the model. Reference --------- Thazin Min, Marta Tibiletti, Paul Hockings, Aleksandra Galetin, Ebony Gunwhy, Gerry Kenna, Nicola Melillo, Geoff JM Parker, Gunnar Schuetz, Daniel Scotcher, John Waterton, Ian Rowe, and Steven Sourbron. *Measurement of liver function with dynamic gadoxetate-enhanced MRI: a validation study in healthy volunteers*. Proc Intl Soc Mag Reson Med, Singapore 2024. .. GENERATED FROM PYTHON SOURCE LINES 44-46 Setup ----- .. GENERATED FROM PYTHON SOURCE LINES 46-55 .. code-block:: Python # Import packages import pandas as pd import matplotlib.pyplot as plt import dcmri as dc # Fetch the data from the TRISTAN rifampicin study: data = dc.fetch('tristan_rifampicin') .. GENERATED FROM PYTHON SOURCE LINES 56-60 Model definition ---------------- In order to avoid some repetition in this script, we define a function that returns a trained model for a single dataset: .. GENERATED FROM PYTHON SOURCE LINES 60-94 .. code-block:: Python def tristan_human_1scan(data, **kwargs): model = dc.AortaLiver( # Injection parameters weight = data['weight'], agent = data['agent'], dose = data['dose'][0], rate = data['rate'], # Acquisition parameters field_strength = data['field_strength'], t0 = data['t0'], TR = data['TR'], FA = data['FA'], # Signal parameters R10a = data['R10b'], R10l = data['R10l'], # Tissue parameters H = data['Hct'], vol = data['vol'], ) xdata = (data['time1aorta'], data['time1liver']) ydata = (data['signal1aorta'], data['signal1liver']) model.train(xdata, ydata, **kwargs) return xdata, ydata, model .. GENERATED FROM PYTHON SOURCE LINES 95-100 Check model fit --------------- Before running the full analysis on all cases, lets illustrate the results by fitting the baseline visit for the first subject. We use maximum verbosity to get some feedback about the iterations: .. GENERATED FROM PYTHON SOURCE LINES 100-103 .. code-block:: Python xdata, ydata, model = tristan_human_1scan(data[0], xtol=1e-3, verbose=2) .. rst-class:: sphx-glr-script-out .. code-block:: none Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 2.4047e+07 1.06e+08 1 2 4.7434e+06 1.93e+07 5.19e+01 1.68e+07 2 3 1.0190e+06 3.72e+06 5.36e+01 1.62e+07 3 4 3.1780e+05 7.01e+05 6.10e+01 8.63e+06 4 5 1.0291e+05 2.15e+05 1.15e+02 2.41e+06 5 6 5.5617e+04 4.73e+04 6.76e+01 1.17e+05 6 7 4.9183e+04 6.43e+03 1.01e+02 9.87e+04 7 8 4.7481e+04 1.70e+03 4.48e+01 9.03e+04 8 10 4.7479e+04 1.75e+00 1.53e+01 6.42e+04 9 11 4.6923e+04 5.55e+02 3.06e+00 1.34e+04 10 12 4.6805e+04 1.18e+02 5.98e+00 4.62e+03 11 14 4.6735e+04 6.96e+01 3.28e+00 2.12e+03 12 15 4.6619e+04 1.16e+02 6.68e+00 1.98e+03 13 18 4.6605e+04 1.40e+01 7.77e-01 1.90e+03 14 20 4.6605e+04 0.00e+00 0.00e+00 1.90e+03 `xtol` termination condition is satisfied. Function evaluations 20, initial cost 2.4047e+07, final cost 4.6605e+04, first-order optimality 1.90e+03. Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 8.3787e+06 5.91e+08 1 2 1.1961e+05 8.26e+06 6.18e+02 3.64e+07 2 3 6.9326e+04 5.03e+04 1.09e+02 1.47e+06 3 4 6.5078e+04 4.25e+03 8.95e+01 6.11e+05 4 5 6.3905e+04 1.17e+03 6.56e+01 2.83e+05 5 6 6.3681e+04 2.24e+02 2.95e+01 5.40e+04 6 7 6.3672e+04 8.97e+00 3.37e+00 7.34e+03 7 8 6.3672e+04 2.52e-02 4.52e-01 2.58e+01 `xtol` termination condition is satisfied. Function evaluations 8, initial cost 8.3787e+06, final cost 6.3672e+04, first-order optimality 2.58e+01. Iteration Total nfev Cost Cost reduction Step norm Optimality 0 1 1.1153e+05 3.99e+06 1 2 1.0908e+05 2.44e+03 1.12e+02 1.08e+05 2 4 1.0887e+05 2.18e+02 7.49e+00 4.85e+03 3 7 1.0884e+05 2.17e+01 8.13e-01 1.57e+03 `xtol` termination condition is satisfied. Function evaluations 7, initial cost 1.1153e+05, final cost 1.0884e+05, first-order optimality 1.57e+03. .. GENERATED FROM PYTHON SOURCE LINES 104-106 Plot the results to check that the model has fitted the data. The plot also shows the concentration in the two liver compartments separately: .. GENERATED FROM PYTHON SOURCE LINES 106-109 .. code-block:: Python model.plot(xdata, ydata) .. image-sg:: /generated/examples/liver/images/sphx_glr_plot_tristan_volunteers_001.png :alt: plot tristan volunteers :srcset: /generated/examples/liver/images/sphx_glr_plot_tristan_volunteers_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 110-113 Print the measured model parameters and any derived parameters. Standard deviations are included as a measure of parameter uncertainty, indicate that all parameters are identified robustly: .. GENERATED FROM PYTHON SOURCE LINES 113-116 .. code-block:: Python model.print_params(round_to=3) .. rst-class:: sphx-glr-script-out .. code-block:: none -------------------------------- Free parameters with their stdev -------------------------------- First bolus arrival time (BAT): 73.6 (1.572) sec Cardiac output (CO): 241.974 (11.015) mL/sec Heart-lung mean transit time (Thl): 20.113 (2.391) sec Heart-lung dispersion (Dhl): 0.612 (0.033) Organs blood mean transit time (To): 24.469 (0.718) sec Organs extraction fraction (Eo): 0.125 (0.003) Organs extravascular mean transit time (Toe): 685.087 (30.234) sec Body extraction fraction (Eb): 0.04 (0.005) Liver extracellular volume fraction (ve): 0.463 (0.015) mL/cm3 Extracellular mean transit time (Te): 60.0 (2.832) sec Extracellular dispersion (De): 0.845 (0.015) Hepatocellular uptake rate (khe): 0.005 (0.0) mL/sec/cm3 Hepatocellular mean transit time (Th): 2585.334 (48.31) sec ---------------------------- Fixed and derived parameters ---------------------------- Hematocrit (H): 0.45 Biliary tissue excretion rate (Kbh): 0.0 mL/sec/cm3 Hepatocellular tissue uptake rate (Khe): 0.011 mL/sec/cm3 Biliary excretion rate (kbh): 0.0 mL/sec/cm3 Liver blood clearance (CL): 5.695 mL/sec .. GENERATED FROM PYTHON SOURCE LINES 117-123 Fit all data ------------ Now that we have illustrated an individual result in some detail, we proceed with fitting the data for all 10 volunteers, at baseline and rifampicin visit. We do not print output for these individual computations and instead store results in one single dataframe: .. GENERATED FROM PYTHON SOURCE LINES 123-151 .. code-block:: Python results = [] # Loop over all datasets for scan in data: # Generate a trained model for the scan: _, _, model = tristan_human_1scan(scan, xtol=1e-3) # Save fitted parameters as a dataframe. pars = model.export_params() pars = pd.DataFrame.from_dict(pars, orient = 'index', columns = ["name", "value", "unit", 'stdev']) pars['parameter'] = pars.index pars['visit'] = scan['visit'] pars['subject'] = scan['subject'] # Add the dataframe to the list of results results.append(pars) # Combine all results into a single dataframe. results = pd.concat(results).reset_index(drop=True) # Print all results print(results.to_string()) .. rst-class:: sphx-glr-script-out .. code-block:: none name value unit stdev parameter visit subject 0 First bolus arrival time 73.599907 sec 1.572440 BAT baseline 001 1 Cardiac output 241.974327 mL/sec 11.015050 CO baseline 001 2 Heart-lung mean transit time 20.112552 sec 2.390973 Thl baseline 001 3 Heart-lung dispersion 0.611623 0.033091 Dhl baseline 001 4 Organs blood mean transit time 24.469245 sec 0.718152 To baseline 001 5 Organs extraction fraction 0.124928 0.003282 Eo baseline 001 6 Organs extravascular mean transit time 685.086720 sec 30.234223 Toe baseline 001 7 Body extraction fraction 0.039800 0.004802 Eb baseline 001 8 Hematocrit 0.450000 0.000000 H baseline 001 9 Liver extracellular volume fraction 0.463087 mL/cm3 0.014638 ve baseline 001 10 Extracellular mean transit time 60.000000 sec 2.832045 Te baseline 001 11 Extracellular dispersion 0.844907 0.014775 De baseline 001 12 Hepatocellular uptake rate 0.005149 mL/sec/cm3 0.000045 khe baseline 001 13 Hepatocellular mean transit time 2585.333870 sec 48.310002 Th baseline 001 14 Biliary tissue excretion rate 0.000387 mL/sec/cm3 0.000000 Kbh baseline 001 15 Hepatocellular tissue uptake rate 0.011118 mL/sec/cm3 0.000000 Khe baseline 001 16 Biliary excretion rate 0.000208 mL/sec/cm3 0.000000 kbh baseline 001 17 Liver blood clearance 5.695415 mL/sec 0.000000 CL baseline 001 18 First bolus arrival time 81.123554 sec 0.620984 BAT baseline 002 19 Cardiac output 108.782150 mL/sec 7.095553 CO baseline 002 20 Heart-lung mean transit time 13.773415 sec 1.775889 Thl baseline 002 21 Heart-lung dispersion 0.455787 0.028777 Dhl baseline 002 22 Organs blood mean transit time 16.150140 sec 3.077245 To baseline 002 23 Organs extraction fraction 0.274097 0.015569 Eo baseline 002 24 Organs extravascular mean transit time 339.511622 sec 30.363898 Toe baseline 002 25 Body extraction fraction 0.011039 0.005590 Eb baseline 002 26 Hematocrit 0.450000 0.000000 H baseline 002 27 Liver extracellular volume fraction 0.213326 mL/cm3 15.463144 ve baseline 002 28 Extracellular mean transit time 59.998057 sec 3782.907718 Te baseline 002 29 Extracellular dispersion 0.872680 8.001178 De baseline 002 30 Hepatocellular uptake rate 0.007161 mL/sec/cm3 0.020356 khe baseline 002 31 Hepatocellular mean transit time 1371.863816 sec 98.407975 Th baseline 002 32 Biliary tissue excretion rate 0.000729 mL/sec/cm3 0.000000 Kbh baseline 002 33 Hepatocellular tissue uptake rate 0.033570 mL/sec/cm3 0.000000 Khe baseline 002 34 Biliary excretion rate 0.000573 mL/sec/cm3 0.000000 kbh baseline 002 35 Liver blood clearance 4.896061 mL/sec 0.000000 CL baseline 002 36 First bolus arrival time 72.507208 sec 0.860429 BAT baseline 003 37 Cardiac output 128.739498 mL/sec 3.736899 CO baseline 003 38 Heart-lung mean transit time 12.891353 sec 1.424240 Thl baseline 003 39 Heart-lung dispersion 0.430157 0.027247 Dhl baseline 003 40 Organs blood mean transit time 20.158477 sec 2.129232 To baseline 003 41 Organs extraction fraction 0.131104 0.009426 Eo baseline 003 42 Organs extravascular mean transit time 286.271133 sec 24.622326 Toe baseline 003 43 Body extraction fraction 0.074352 0.003885 Eb baseline 003 44 Hematocrit 0.450000 0.000000 H baseline 003 45 Liver extracellular volume fraction 0.190146 mL/cm3 0.081793 ve baseline 003 46 Extracellular mean transit time 28.501686 sec 13.998832 Te baseline 003 47 Extracellular dispersion 0.769657 0.150600 De baseline 003 48 Hepatocellular uptake rate 0.008714 mL/sec/cm3 0.000215 khe baseline 003 49 Hepatocellular mean transit time 2612.595078 sec 143.289866 Th baseline 003 50 Biliary tissue excretion rate 0.000383 mL/sec/cm3 0.000000 Kbh baseline 003 51 Hepatocellular tissue uptake rate 0.045826 mL/sec/cm3 0.000000 Khe baseline 003 52 Biliary excretion rate 0.000310 mL/sec/cm3 0.000000 kbh baseline 003 53 Liver blood clearance 7.616406 mL/sec 0.000000 CL baseline 003 54 First bolus arrival time 76.650272 sec 0.348343 BAT baseline 004 55 Cardiac output 68.050254 mL/sec 1.274909 CO baseline 004 56 Heart-lung mean transit time 6.673474 sec 0.481736 Thl baseline 004 57 Heart-lung dispersion 0.803749 0.033215 Dhl baseline 004 58 Organs blood mean transit time 35.927221 sec 1.713336 To baseline 004 59 Organs extraction fraction 0.295439 0.008891 Eo baseline 004 60 Organs extravascular mean transit time 506.858853 sec 37.637641 Toe baseline 004 61 Body extraction fraction 0.150000 0.008696 Eb baseline 004 62 Hematocrit 0.450000 0.000000 H baseline 004 63 Liver extracellular volume fraction 0.091126 mL/cm3 0.191224 ve baseline 004 64 Extracellular mean transit time 59.999948 sec 103.973489 Te baseline 004 65 Extracellular dispersion 0.869812 0.217073 De baseline 004 66 Hepatocellular uptake rate 0.003447 mL/sec/cm3 0.000054 khe baseline 004 67 Hepatocellular mean transit time 17647.890812 sec 4146.439098 Th baseline 004 68 Biliary tissue excretion rate 0.000057 mL/sec/cm3 0.000000 Kbh baseline 004 69 Hepatocellular tissue uptake rate 0.037825 mL/sec/cm3 0.000000 Khe baseline 004 70 Biliary excretion rate 0.000052 mL/sec/cm3 0.000000 kbh baseline 004 71 Liver blood clearance 3.054051 mL/sec 0.000000 CL baseline 004 72 First bolus arrival time 77.664043 sec 1.636269 BAT baseline 005 73 Cardiac output 144.663585 mL/sec 6.778782 CO baseline 005 74 Heart-lung mean transit time 11.780140 sec 2.470655 Thl baseline 005 75 Heart-lung dispersion 0.512869 0.050748 Dhl baseline 005 76 Organs blood mean transit time 16.661301 sec 1.734136 To baseline 005 77 Organs extraction fraction 0.171204 0.012378 Eo baseline 005 78 Organs extravascular mean transit time 266.218039 sec 21.826471 Toe baseline 005 79 Body extraction fraction 0.048306 0.004197 Eb baseline 005 80 Hematocrit 0.450000 0.000000 H baseline 005 81 Liver extracellular volume fraction 0.339997 mL/cm3 0.051949 ve baseline 005 82 Extracellular mean transit time 50.848739 sec 10.159249 Te baseline 005 83 Extracellular dispersion 0.879072 0.040737 De baseline 005 84 Hepatocellular uptake rate 0.006272 mL/sec/cm3 0.000170 khe baseline 005 85 Hepatocellular mean transit time 1680.281504 sec 67.030238 Th baseline 005 86 Biliary tissue excretion rate 0.000595 mL/sec/cm3 0.000000 Kbh baseline 005 87 Hepatocellular tissue uptake rate 0.018449 mL/sec/cm3 0.000000 Khe baseline 005 88 Biliary excretion rate 0.000393 mL/sec/cm3 0.000000 kbh baseline 005 89 Liver blood clearance 4.424120 mL/sec 0.000000 CL baseline 005 90 First bolus arrival time 71.414398 sec 1.800219 BAT baseline 006 91 Cardiac output 87.000607 mL/sec 6.545973 CO baseline 006 92 Heart-lung mean transit time 14.992117 sec 1.484213 Thl baseline 006 93 Heart-lung dispersion 0.351066 0.029522 Dhl baseline 006 94 Organs blood mean transit time 31.915969 sec 2.016451 To baseline 006 95 Organs extraction fraction 0.216771 0.018967 Eo baseline 006 96 Organs extravascular mean transit time 317.629112 sec 34.737274 Toe baseline 006 97 Body extraction fraction 0.067939 0.009687 Eb baseline 006 98 Hematocrit 0.450000 0.000000 H baseline 006 99 Liver extracellular volume fraction 0.319999 mL/cm3 0.074208 ve baseline 006 100 Extracellular mean transit time 59.739420 sec 13.698991 Te baseline 006 101 Extracellular dispersion 0.751767 0.063386 De baseline 006 102 Hepatocellular uptake rate 0.007392 mL/sec/cm3 0.000208 khe baseline 006 103 Hepatocellular mean transit time 2258.348723 sec 115.924096 Th baseline 006 104 Biliary tissue excretion rate 0.000443 mL/sec/cm3 0.000000 Kbh baseline 006 105 Hepatocellular tissue uptake rate 0.023100 mL/sec/cm3 0.000000 Khe baseline 006 106 Biliary excretion rate 0.000301 mL/sec/cm3 0.000000 kbh baseline 006 107 Liver blood clearance 5.109034 mL/sec 0.000000 CL baseline 006 108 First bolus arrival time 71.382701 sec 0.669215 BAT baseline 007 109 Cardiac output 122.547754 mL/sec 2.617794 CO baseline 007 110 Heart-lung mean transit time 9.066438 sec 0.732294 Thl baseline 007 111 Heart-lung dispersion 0.295320 0.018564 Dhl baseline 007 112 Organs blood mean transit time 25.603369 sec 1.384952 To baseline 007 113 Organs extraction fraction 0.190775 0.007632 Eo baseline 007 114 Organs extravascular mean transit time 488.642798 sec 25.171671 Toe baseline 007 115 Body extraction fraction 0.035468 0.002685 Eb baseline 007 116 Hematocrit 0.450000 0.000000 H baseline 007 117 Liver extracellular volume fraction 0.074030 mL/cm3 0.043702 ve baseline 007 118 Extracellular mean transit time 59.999998 sec 17.044384 Te baseline 007 119 Extracellular dispersion 1.000000 0.068193 De baseline 007 120 Hepatocellular uptake rate 0.005601 mL/sec/cm3 0.000115 khe baseline 007 121 Hepatocellular mean transit time 1944.884802 sec 77.919396 Th baseline 007 122 Biliary tissue excretion rate 0.000514 mL/sec/cm3 0.000000 Kbh baseline 007 123 Hepatocellular tissue uptake rate 0.075655 mL/sec/cm3 0.000000 Khe baseline 007 124 Biliary excretion rate 0.000476 mL/sec/cm3 0.000000 kbh baseline 007 125 Liver blood clearance 5.288011 mL/sec 0.000000 CL baseline 007 126 First bolus arrival time 75.441599 sec 0.661646 BAT baseline 008 127 Cardiac output 223.684233 mL/sec 5.069377 CO baseline 008 128 Heart-lung mean transit time 15.854049 sec 0.824588 Thl baseline 008 129 Heart-lung dispersion 0.339042 0.013839 Dhl baseline 008 130 Organs blood mean transit time 14.687171 sec 1.166190 To baseline 008 131 Organs extraction fraction 0.142962 0.006737 Eo baseline 008 132 Organs extravascular mean transit time 366.963612 sec 23.312960 Toe baseline 008 133 Body extraction fraction 0.033847 0.002074 Eb baseline 008 134 Hematocrit 0.450000 0.000000 H baseline 008 135 Liver extracellular volume fraction 0.208483 mL/cm3 0.025349 ve baseline 008 136 Extracellular mean transit time 21.575379 sec 3.659178 Te baseline 008 137 Extracellular dispersion 0.611710 0.084386 De baseline 008 138 Hepatocellular uptake rate 0.006767 mL/sec/cm3 0.000143 khe baseline 008 139 Hepatocellular mean transit time 1578.020505 sec 54.555972 Th baseline 008 140 Biliary tissue excretion rate 0.000634 mL/sec/cm3 0.000000 Kbh baseline 008 141 Hepatocellular tissue uptake rate 0.032456 mL/sec/cm3 0.000000 Khe baseline 008 142 Biliary excretion rate 0.000502 mL/sec/cm3 0.000000 kbh baseline 008 143 Liver blood clearance 6.964833 mL/sec 0.000000 CL baseline 008 144 First bolus arrival time 71.678276 sec 0.569448 BAT baseline 009 145 Cardiac output 194.498276 mL/sec 3.941457 CO baseline 009 146 Heart-lung mean transit time 18.201927 sec 0.671778 Thl baseline 009 147 Heart-lung dispersion 0.422045 0.013446 Dhl baseline 009 148 Organs blood mean transit time 26.211463 sec 1.250171 To baseline 009 149 Organs extraction fraction 0.125443 0.005706 Eo baseline 009 150 Organs extravascular mean transit time 469.859132 sec 32.380451 Toe baseline 009 151 Body extraction fraction 0.058306 0.002504 Eb baseline 009 152 Hematocrit 0.450000 0.000000 H baseline 009 153 Liver extracellular volume fraction 0.146019 mL/cm3 0.018307 ve baseline 009 154 Extracellular mean transit time 27.765372 sec 5.410730 Te baseline 009 155 Extracellular dispersion 0.714619 0.082420 De baseline 009 156 Hepatocellular uptake rate 0.003476 mL/sec/cm3 0.000069 khe baseline 009 157 Hepatocellular mean transit time 2048.448396 sec 68.842894 Th baseline 009 158 Biliary tissue excretion rate 0.000488 mL/sec/cm3 0.000000 Kbh baseline 009 159 Hepatocellular tissue uptake rate 0.023808 mL/sec/cm3 0.000000 Khe baseline 009 160 Biliary excretion rate 0.000417 mL/sec/cm3 0.000000 kbh baseline 009 161 Liver blood clearance 4.123449 mL/sec 0.000000 CL baseline 009 162 First bolus arrival time 67.651089 sec 0.655125 BAT baseline 010 163 Cardiac output 102.969939 mL/sec 1.282155 CO baseline 010 164 Heart-lung mean transit time 20.229862 sec 0.726057 Thl baseline 010 165 Heart-lung dispersion 0.303307 0.009591 Dhl baseline 010 166 Organs blood mean transit time 36.877025 sec 1.486028 To baseline 010 167 Organs extraction fraction 0.152260 0.003926 Eo baseline 010 168 Organs extravascular mean transit time 794.361050 sec 53.689872 Toe baseline 010 169 Body extraction fraction 0.034530 0.003043 Eb baseline 010 170 Hematocrit 0.450000 0.000000 H baseline 010 171 Liver extracellular volume fraction 0.093810 mL/cm3 0.089926 ve baseline 010 172 Extracellular mean transit time 59.999986 sec 42.216733 Te baseline 010 173 Extracellular dispersion 0.947458 0.054017 De baseline 010 174 Hepatocellular uptake rate 0.004102 mL/sec/cm3 0.000081 khe baseline 010 175 Hepatocellular mean transit time 2006.021673 sec 59.261211 Th baseline 010 176 Biliary tissue excretion rate 0.000498 mL/sec/cm3 0.000000 Kbh baseline 010 177 Hepatocellular tissue uptake rate 0.043730 mL/sec/cm3 0.000000 Khe baseline 010 178 Biliary excretion rate 0.000452 mL/sec/cm3 0.000000 kbh baseline 010 179 Liver blood clearance 4.413661 mL/sec 0.000000 CL baseline 010 180 First bolus arrival time 77.704296 sec 0.836351 BAT rifampicin 002 181 Cardiac output 122.008090 mL/sec 7.727259 CO rifampicin 002 182 Heart-lung mean transit time 11.939837 sec 1.989499 Thl rifampicin 002 183 Heart-lung dispersion 0.466967 0.035088 Dhl rifampicin 002 184 Organs blood mean transit time 18.293255 sec 3.367993 To rifampicin 002 185 Organs extraction fraction 0.130616 0.011235 Eo rifampicin 002 186 Organs extravascular mean transit time 314.803679 sec 39.887405 Toe rifampicin 002 187 Body extraction fraction 0.043948 0.004700 Eb rifampicin 002 188 Hematocrit 0.450000 0.000000 H rifampicin 002 189 Liver extracellular volume fraction 0.172314 mL/cm3 0.015963 ve rifampicin 002 190 Extracellular mean transit time 32.221249 sec 6.491459 Te rifampicin 002 191 Extracellular dispersion 0.691793 0.091270 De rifampicin 002 192 Hepatocellular uptake rate 0.000496 mL/sec/cm3 0.000050 khe rifampicin 002 193 Hepatocellular mean transit time 35999.962190 sec 101296.318105 Th rifampicin 002 194 Biliary tissue excretion rate 0.000028 mL/sec/cm3 0.000000 Kbh rifampicin 002 195 Hepatocellular tissue uptake rate 0.002881 mL/sec/cm3 0.000000 Khe rifampicin 002 196 Biliary excretion rate 0.000023 mL/sec/cm3 0.000000 kbh rifampicin 002 197 Liver blood clearance 0.398354 mL/sec 0.000000 CL rifampicin 002 198 First bolus arrival time 68.040902 sec 0.704690 BAT rifampicin 003 199 Cardiac output 129.150719 mL/sec 4.891854 CO rifampicin 003 200 Heart-lung mean transit time 11.072115 sec 0.706199 Thl rifampicin 003 201 Heart-lung dispersion 0.307993 0.016601 Dhl rifampicin 003 202 Organs blood mean transit time 18.267877 sec 1.048446 To rifampicin 003 203 Organs extraction fraction 0.117154 0.011605 Eo rifampicin 003 204 Organs extravascular mean transit time 228.523202 sec 26.292208 Toe rifampicin 003 205 Body extraction fraction 0.041062 0.002620 Eb rifampicin 003 206 Hematocrit 0.450000 0.000000 H rifampicin 003 207 Liver extracellular volume fraction 0.207746 mL/cm3 0.012765 ve rifampicin 003 208 Extracellular mean transit time 25.775441 sec 3.119655 Te rifampicin 003 209 Extracellular dispersion 0.656847 0.056295 De rifampicin 003 210 Hepatocellular uptake rate 0.000520 mL/sec/cm3 0.000040 khe rifampicin 003 211 Hepatocellular mean transit time 35999.990609 sec 77637.941865 Th rifampicin 003 212 Biliary tissue excretion rate 0.000028 mL/sec/cm3 0.000000 Kbh rifampicin 003 213 Hepatocellular tissue uptake rate 0.002504 mL/sec/cm3 0.000000 Khe rifampicin 003 214 Biliary excretion rate 0.000022 mL/sec/cm3 0.000000 kbh rifampicin 003 215 Liver blood clearance 0.448360 mL/sec 0.000000 CL rifampicin 003 216 First bolus arrival time 65.518708 sec 0.072409 BAT rifampicin 004 217 Cardiac output 95.671426 mL/sec 0.923749 CO rifampicin 004 218 Heart-lung mean transit time 17.419474 sec 0.157633 Thl rifampicin 004 219 Heart-lung dispersion 0.437536 0.004343 Dhl rifampicin 004 220 Organs blood mean transit time 43.528453 sec 1.212983 To rifampicin 004 221 Organs extraction fraction 0.226562 0.004587 Eo rifampicin 004 222 Organs extravascular mean transit time 503.131788 sec 27.406610 Toe rifampicin 004 223 Body extraction fraction 0.031694 0.002992 Eb rifampicin 004 224 Hematocrit 0.450000 0.000000 H rifampicin 004 225 Liver extracellular volume fraction 0.196081 mL/cm3 0.007320 ve rifampicin 004 226 Extracellular mean transit time 60.000000 sec 3.972009 Te rifampicin 004 227 Extracellular dispersion 0.802130 0.022059 De rifampicin 004 228 Hepatocellular uptake rate 0.000303 mL/sec/cm3 0.000028 khe rifampicin 004 229 Hepatocellular mean transit time 5407.181386 sec 2279.508644 Th rifampicin 004 230 Biliary tissue excretion rate 0.000185 mL/sec/cm3 0.000000 Kbh rifampicin 004 231 Hepatocellular tissue uptake rate 0.001546 mL/sec/cm3 0.000000 Khe rifampicin 004 232 Biliary excretion rate 0.000149 mL/sec/cm3 0.000000 kbh rifampicin 004 233 Liver blood clearance 0.298156 mL/sec 0.000000 CL rifampicin 004 234 First bolus arrival time 70.554777 sec 0.690494 BAT rifampicin 006 235 Cardiac output 148.624938 mL/sec 3.989927 CO rifampicin 006 236 Heart-lung mean transit time 15.422488 sec 0.683854 Thl rifampicin 006 237 Heart-lung dispersion 0.308703 0.012320 Dhl rifampicin 006 238 Organs blood mean transit time 20.106424 sec 0.940140 To rifampicin 006 239 Organs extraction fraction 0.130751 0.006790 Eo rifampicin 006 240 Organs extravascular mean transit time 379.541275 sec 33.038080 Toe rifampicin 006 241 Body extraction fraction 0.021857 0.002348 Eb rifampicin 006 242 Hematocrit 0.450000 0.000000 H rifampicin 006 243 Liver extracellular volume fraction 0.294997 mL/cm3 0.012491 ve rifampicin 006 244 Extracellular mean transit time 39.624816 sec 3.136944 Te rifampicin 006 245 Extracellular dispersion 0.677593 0.034950 De rifampicin 006 246 Hepatocellular uptake rate 0.000253 mL/sec/cm3 0.000041 khe rifampicin 006 247 Hepatocellular mean transit time 35999.999925 sec 174271.569796 Th rifampicin 006 248 Biliary tissue excretion rate 0.000028 mL/sec/cm3 0.000000 Kbh rifampicin 006 249 Hepatocellular tissue uptake rate 0.000859 mL/sec/cm3 0.000000 Khe rifampicin 006 250 Biliary excretion rate 0.000020 mL/sec/cm3 0.000000 kbh rifampicin 006 251 Liver blood clearance 0.178868 mL/sec 0.000000 CL rifampicin 006 252 First bolus arrival time 66.981669 sec 0.447870 BAT rifampicin 007 253 Cardiac output 121.108337 mL/sec 2.431132 CO rifampicin 007 254 Heart-lung mean transit time 12.405541 sec 0.468920 Thl rifampicin 007 255 Heart-lung dispersion 0.320329 0.010899 Dhl rifampicin 007 256 Organs blood mean transit time 18.751282 sec 0.906336 To rifampicin 007 257 Organs extraction fraction 0.178401 0.008336 Eo rifampicin 007 258 Organs extravascular mean transit time 258.378788 sec 15.783747 Toe rifampicin 007 259 Body extraction fraction 0.040531 0.001594 Eb rifampicin 007 260 Hematocrit 0.450000 0.000000 H rifampicin 007 261 Liver extracellular volume fraction 0.173631 mL/cm3 0.008107 ve rifampicin 007 262 Extracellular mean transit time 46.520097 sec 4.249694 Te rifampicin 007 263 Extracellular dispersion 0.768998 0.035040 De rifampicin 007 264 Hepatocellular uptake rate 0.000259 mL/sec/cm3 0.000022 khe rifampicin 007 265 Hepatocellular mean transit time 35999.982870 sec 72376.569654 Th rifampicin 007 266 Biliary tissue excretion rate 0.000028 mL/sec/cm3 0.000000 Kbh rifampicin 007 267 Hepatocellular tissue uptake rate 0.001489 mL/sec/cm3 0.000000 Khe rifampicin 007 268 Biliary excretion rate 0.000023 mL/sec/cm3 0.000000 kbh rifampicin 007 269 Liver blood clearance 0.288395 mL/sec 0.000000 CL rifampicin 007 270 First bolus arrival time 72.506204 sec 0.665511 BAT rifampicin 008 271 Cardiac output 189.368130 mL/sec 4.517157 CO rifampicin 008 272 Heart-lung mean transit time 14.708482 sec 1.044477 Thl rifampicin 008 273 Heart-lung dispersion 0.423958 0.017040 Dhl rifampicin 008 274 Organs blood mean transit time 18.022003 sec 1.130311 To rifampicin 008 275 Organs extraction fraction 0.092802 0.003435 Eo rifampicin 008 276 Organs extravascular mean transit time 619.577533 sec 45.448472 Toe rifampicin 008 277 Body extraction fraction 0.016752 0.001728 Eb rifampicin 008 278 Hematocrit 0.450000 0.000000 H rifampicin 008 279 Liver extracellular volume fraction 0.152334 mL/cm3 0.008524 ve rifampicin 008 280 Extracellular mean transit time 25.777303 sec 2.847915 Te rifampicin 008 281 Extracellular dispersion 0.538127 0.070221 De rifampicin 008 282 Hepatocellular uptake rate 0.000251 mL/sec/cm3 0.000024 khe rifampicin 008 283 Hepatocellular mean transit time 35999.999833 sec 79392.913259 Th rifampicin 008 284 Biliary tissue excretion rate 0.000028 mL/sec/cm3 0.000000 Kbh rifampicin 008 285 Hepatocellular tissue uptake rate 0.001649 mL/sec/cm3 0.000000 Khe rifampicin 008 286 Biliary excretion rate 0.000024 mL/sec/cm3 0.000000 kbh rifampicin 008 287 Liver blood clearance 0.221231 mL/sec 0.000000 CL rifampicin 008 288 First bolus arrival time 80.302388 sec 1.211241 BAT rifampicin 009 289 Cardiac output 177.476568 mL/sec 4.810968 CO rifampicin 009 290 Heart-lung mean transit time 13.750619 sec 1.465945 Thl rifampicin 009 291 Heart-lung dispersion 0.697022 0.054634 Dhl rifampicin 009 292 Organs blood mean transit time 47.519313 sec 1.672592 To rifampicin 009 293 Organs extraction fraction 0.101424 0.003632 Eo rifampicin 009 294 Organs extravascular mean transit time 767.431272 sec 87.878979 Toe rifampicin 009 295 Body extraction fraction 0.019406 0.003808 Eb rifampicin 009 296 Hematocrit 0.450000 0.000000 H rifampicin 009 297 Liver extracellular volume fraction 0.201192 mL/cm3 0.009351 ve rifampicin 009 298 Extracellular mean transit time 58.583425 sec 5.343677 Te rifampicin 009 299 Extracellular dispersion 0.719176 0.041223 De rifampicin 009 300 Hepatocellular uptake rate 0.000173 mL/sec/cm3 0.000031 khe rifampicin 009 301 Hepatocellular mean transit time 4537.539297 sec 2736.133967 Th rifampicin 009 302 Biliary tissue excretion rate 0.000220 mL/sec/cm3 0.000000 Kbh rifampicin 009 303 Hepatocellular tissue uptake rate 0.000859 mL/sec/cm3 0.000000 Khe rifampicin 009 304 Biliary excretion rate 0.000176 mL/sec/cm3 0.000000 kbh rifampicin 009 305 Liver blood clearance 0.207461 mL/sec 0.000000 CL rifampicin 009 306 First bolus arrival time 79.441638 sec 2.820043 BAT rifampicin 010 307 Cardiac output 112.555304 mL/sec 7.002948 CO rifampicin 010 308 Heart-lung mean transit time 21.589344 sec 2.763996 Thl rifampicin 010 309 Heart-lung dispersion 0.527503 0.048222 Dhl rifampicin 010 310 Organs blood mean transit time 40.942396 sec 1.672576 To rifampicin 010 311 Organs extraction fraction 0.157990 0.007099 Eo rifampicin 010 312 Organs extravascular mean transit time 788.213403 sec 78.019202 Toe rifampicin 010 313 Body extraction fraction 0.025112 0.007208 Eb rifampicin 010 314 Hematocrit 0.450000 0.000000 H rifampicin 010 315 Liver extracellular volume fraction 0.210117 mL/cm3 0.010655 ve rifampicin 010 316 Extracellular mean transit time 52.993789 sec 4.731529 Te rifampicin 010 317 Extracellular dispersion 0.625601 0.045104 De rifampicin 010 318 Hepatocellular uptake rate 0.000236 mL/sec/cm3 0.000035 khe rifampicin 010 319 Hepatocellular mean transit time 4895.303568 sec 2471.354757 Th rifampicin 010 320 Biliary tissue excretion rate 0.000204 mL/sec/cm3 0.000000 Kbh rifampicin 010 321 Hepatocellular tissue uptake rate 0.001121 mL/sec/cm3 0.000000 Khe rifampicin 010 322 Biliary excretion rate 0.000161 mL/sec/cm3 0.000000 kbh rifampicin 010 323 Liver blood clearance 0.261218 mL/sec 0.000000 CL rifampicin 010 .. GENERATED FROM PYTHON SOURCE LINES 152-157 Plot individual results ----------------------- Now lets visualise the main results from the study by plotting the drug effect for all volunteers, and for both biomarkers: uptake rate ``khe`` and excretion rate ``kbh``: .. GENERATED FROM PYTHON SOURCE LINES 157-197 .. code-block:: Python # Set up the figure clr = ['tab:blue', 'tab:orange', 'tab:green', 'tab:red', 'tab:purple', 'tab:brown', 'tab:pink', 'tab:gray', 'tab:olive', 'tab:cyan'] fs = 10 fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(8,3)) fig.subplots_adjust(wspace=0.5) ax1.set_title('Hepatocellular uptake rate', fontsize=fs, pad=10) ax1.set_ylabel('khe (mL/min/100mL)', fontsize=fs) ax1.set_ylim(0, 60) ax1.tick_params(axis='x', labelsize=fs) ax1.tick_params(axis='y', labelsize=fs) ax2.set_title('Biliary excretion rate', fontsize=fs, pad=10) ax2.set_ylabel('kbh (mL/min/100mL)', fontsize=fs) ax2.set_ylim(0, 6) ax2.tick_params(axis='x', labelsize=fs) ax2.tick_params(axis='y', labelsize=fs) # Pivot data for both visits to wide format for easy access: v1 = pd.pivot_table(results[results.visit=='baseline'], values='value', columns='parameter', index='subject') v2 = pd.pivot_table(results[results.visit=='rifampicin'], values='value', columns='parameter', index='subject') # Plot the rate constants in units of mL/min/100mL for s in v1.index: x = ['baseline'] khe = [6000*v1.at[s,'khe']] kbh = [6000*v1.at[s,'kbh']] if s in v2.index: x += ['rifampicin'] khe += [6000*v2.at[s,'khe']] kbh += [6000*v2.at[s,'kbh']] color = clr[int(s)-1] ax1.plot(x, khe, '-', label=s, marker='o', markersize=6, color=color) ax2.plot(x, kbh, '-', label=s, marker='o', markersize=6, color=color) plt.show() # Choose the last image as a thumbnail for the gallery # sphinx_gallery_thumbnail_number = -1 .. image-sg:: /generated/examples/liver/images/sphx_glr_plot_tristan_volunteers_002.png :alt: Hepatocellular uptake rate, Biliary excretion rate :srcset: /generated/examples/liver/images/sphx_glr_plot_tristan_volunteers_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** (13 minutes 2.585 seconds) .. _sphx_glr_download_generated_examples_liver_plot_tristan_volunteers.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_tristan_volunteers.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_tristan_volunteers.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_tristan_volunteers.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_