Abstract
Analysis of fluorescence lifetime imaging microscopy (FLIM) and Förster resonance energy transfer (FRET) experiments in living cells is usually based on mean lifetimes computations. However, these mean lifetimes can induce misinterpretations. We propose in this work the implementation of the transportation distance for FLIM and FRET experiments in vivo. This non-fitting indicator, which is easy to compute, reflects the similarity between two distributions and can be used for pixels clustering to improve the estimation of the FRET parameters. We study the robustness and the discriminating power of this transportation distance, both theoretically and numerically. In addition, a comparison study with the largely used mean lifetime differences is performed. We finally demonstrate practically the benefits of the transportation distance over the usual mean lifetime differences for both FLIM and FRET experiments in living cells.
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Acknowledgments
We thank Franck Riquet (University of Lille1), Francois Sipieter (University of Lille1) and Céline Schulz (IRI) for creating the memb-eGFP and CFP-Venus plasmids. We are grateful to Olivier Bensaude (IBENS) for kindly providing us with the HEXIM1-CFP plasmid.
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This work was funded by the CNRS, the Région Nord-Pas de Calais, the European Regional Developmental Funds (CPER CIA 2007–2013), the French Research Agency (ANR-12-BSV5-0018), a Leica Microsystems partnership and the French network in microscopy GDR2588. This work was also supported in part by the national large loans ”Equipex” (ImaginEx BioMed) and ”Labex” CEMPI (ANR-11-LABX-0007-01).
Appendices
Appendix A: Expressing \(d_{\text {trans}}(S,{{S}^\mathrm {b}})\) and Comparing with \(d_{\text {int}}(S,{{S}^\mathrm {b}})\)
1.1 In Case where \(\mathsf {T}=\infty \)
This theoretical study is restricted to \(\mathsf {T}=\infty \) ; for truncated exponential functions (see below), the sign of some expressions involved is much more complicated to grasp. For now, assume that
If \(\varphi _1 =1\), we have
whereas if \(\tau _1 ={{\tau _1}^\mathrm {b}}\), we have
Under conditions \(\underline{\tau _1={{\tau _1}^\mathrm {b}},\,\varphi _1=1}\): Eq. (20) yields
Under conditions \(\underline{\tau _1<{{\tau _1}^\mathrm {b}},\,\varphi _1=1}\): It is not difficult to see from Eq. (20) that
and we write further
with
Here, we have \(B<0\). If we assume that \(A\le 0\), then \(h(t)\) is always at least \(0\), see Eq. (23) ; otherwise \(A>0\) and we need to compute
so that \(h(t)\) is increasing. The sign of \(h(t)\) will be constant if and only if \(h(0)\ge 0\). Consequently \(d_{\text {trans}}(S,{{S}^\mathrm {b}})\) will match \(d_{\text {int}}(S,{{S}^\mathrm {b}})\) when
Under conditions \(\underline{\tau _1>{{\tau _1}^\mathrm {b}},\,\varphi _1=1}\): In that setting, we have \(B>0\), see Eq. (24). If \(A\ge 0\), then \(h(t)\) stays non-negative. If \(A< 0\), then we see from Eqs. (23) and (25) that \(h'(t)\) is negative and \(h(t)\) decreases. In this case, the sign of \(h(t)\) will be constant if \(h(0)\le 0\). Consequently, \(d_{\text {trans}}(S,{{S}^\mathrm {b}})\) will match \(d_{\text {int}}(S,{{S}^\mathrm {b}})\) when
Under conditions \(\underline{\tau _1={{\tau _1}^\mathrm {b}},\,\tau _2={{\tau _2}^\mathrm {b}}}\): We see from Eq. (21) that the absolute value can be removed so that we always have \(d_{\text {trans}}(S,{{S}^\mathrm {b}}) = d_{\text {int}}(S,{{S}^\mathrm {b}})\).
Under conditions \(\underline{\tau _1={{\tau _1}^\mathrm {b}},\,\tau _1>\tau _2>{{\tau _2}^\mathrm {b}}}\): From Eq. (21), we get
and write further
with
Computing the derivative, we get
and thus \(k(t)\) is monotonic, with \(k(0)=1+\frac{1-{{\varphi _1}^\mathrm {b}}}{\varphi _1-{{\varphi _1}^\mathrm {b}}} \frac{C}{D}\) and \(\lim _{t\rightarrow \infty }k(t)=1\). Thus, \(k(t)\) has a constant sign if and only if \(k(0)\ge 0\), and this is equivalent to
Consequently \(d_{\text {trans}}(S,{{S}^\mathrm {b}})\) will match \(d_{\text {int}}(S,{{S}^\mathrm {b}})\) when
These results are summarized in Table 2.
1.2 In Case where \(\mathsf {T}<\infty \)
In this case, conditions to have \(d_{\text {trans}}=d_{\text {int}}\) are much more complicated to reach mathematically. There are nevertheless easy cases which are worth to mention. Assume that
If \(\varphi _1 =1\), we have
whereas if \(\tau _1 ={{\tau _1}^\mathrm {b}}\), we have
From the fact that for \(B=\mathsf {T}\) and \(A=\mathsf {T}-t>0\), the function
we deduce Table 3 for finite \(\mathsf {T}\).
Appendix B: Confidence Limit for \(d_{\text {trans}}(S_N,S)\): Tools
1.1 Auxillary Lemma
The following result will be of use:
Lemma 1
Assume that for all \(t\in [0,\mathsf {T}]\)
We have for all \(u,t\in [0,\mathsf {T}]\)
-
(i)
\(\int _u^\mathsf {T}S(t)\,dt = \varphi _1\dfrac{\tau _1(\mathrm {e}^{(\mathsf {T}-u)/\tau _1}-1)-(\mathsf {T}-u)}{\mathrm {e}^{\mathsf {T}/\tau _1}-1}+\varphi _2\dfrac{\tau _2(\mathrm {e}^{(\mathsf {T}-u)/\tau _2}-1)-(\mathsf {T}-u)}{\mathrm {e}^{\mathsf {T}/\tau _2}-1}\),
-
(ii)
\(S(t) \le \dfrac{\mathrm {e}^{(\mathsf {T}-t)/\max (\tau _1,\tau _2)}-1}{\mathrm {e}^{\mathsf {T}/\max (\tau _1,\tau _2)}-1}\),
-
(iii)
If we set for \(m>0\),
$$\begin{aligned} \lambda (m)=1-\frac{\arctan \left( \frac{1}{2}\sqrt{\mathrm {e}^{\frac{\mathsf {T}}{m}}-1}\right) }{\frac{1}{2}\sqrt{\mathrm {e}^{\frac{\mathsf {T}}{m}}-1}}+\log \left( \frac{2}{\sqrt{1+3\mathrm {e}^{-\frac{\mathsf {T}}{m}}}}\right) , \end{aligned}$$then,
$$\begin{aligned} \int _0^\mathsf {T}\sqrt{S(t)(1-S(t))}\,dt\le \lambda (\max (\tau _1,\tau _2)) \max (\tau _1,\tau _2)\le (1+\log 2)\max (\tau _1,\tau _2). \end{aligned}$$
Proof
The first assertion (i) follows easily by calculus and (ii) comes from the fact that for \(B> A>0\), the function
For (iii), set for short \(m=\max (\tau _1,\tau _2)\). We bound the integral of (iii) by splitting it in two parts: For any \(u\) in \([0,\mathsf {T}]\), since \(\sqrt{S(t)(1-S(t))}\) is at most one half, and by (ii),
Going on, by the change of variable \(t=\mathsf {T}-m\log (1+x^2)\), we get
and thus
To optimize in \(u\), we set \(u=\mathsf {T}-my\) and introduce the function
whose derivative is
We see then that we have to choose \(y_0\) such that \(\sqrt{\mathrm {e}^{y_0}-1 }=\frac{1}{2} \sqrt{\mathrm {e}^{\mathsf {T}/m}-1}\) which yields
Note by the way that \(\lambda (m)\) is increasing as a function of \(\mathsf {T}\) and consequently bounded by \(\lim _{\mathsf {T}\rightarrow \infty } \lambda (m)=\log 2 +1\).
1.2 Asymptotic Behavior of \(d_{\text {trans}}(S_N,S)\): Approximate Confidence Limit
Provided that \(S\) is sufficiently integrable (which is the case for our truncated exponential models given by Eq. 5), a straightforward consequence of the central limit theorem for empirical processes in \(L^1(\mathbb {R})\) (Del Barrio et al. 1999, Theorem 2.1) is
or less formally,
where \(\{B_u,u\in [0,1]\}\) is a standard Brownian bridge, that is, a centered Gaussian process on \([0,1]\) with covariance function \(\mathbf {E}(B_uB_v)=\min (u,v)-uv\) (convergence of moments is also true, see (Del Barrio et al. 1999, Theorem 2.4a)). Furthermore, since for each \(t\), \(B_{S(t)}\) is a centered Gaussian random variable with variance \(S(t)(1-S(t))\),
Thus, by Lemma 1 (iii),
Besides, the Gaussian deviation inequality (Ledoux 1994, Corollary 1) applied in the separable Banach space \(L^1(\mathbb {R}_+)\) (whose dual space is \(L^\infty (\mathbb {R}_+)\)) gives for all positive \(u\),
with a deviation parameter \(\sigma ^2\) which is tractable:
where we set for short
with \([0,1]\)-valued and increasing functions
A small study of variations shows that for \(x\le \mathsf {T}\), we have \(\eta (x)\le \rho (x)^2\) so that \(\eta _i\le \rho _i^2\) and from Eq. (31)
Moreover, it is not difficult to see that, for \(a,b>0\), the maximum of the function \(\varphi \mapsto 2(\varphi a^2+(1-\varphi )b^2)-(\varphi a+(1-\varphi )b)^2\) on \([0,1]\) is \((\max (a,b))^2\). Consequently, Eq. (32) gives
since \(\rho (x)\) is increasing. Now, if we set \(u=\sigma \sqrt{2x}\) in Eq. (30) and use Eqs. (29) and (33), we get
By combining Eqs. (28) and (34), we get that with probability at least \(1-\mathrm {e}^{-x}\)
Note the dependence in \(\mathsf {T}\) of Eq. (35). Actually, the bound Eq. (35) is increasing with respect to \(\mathsf {T}\) and Eq. (36) corresponds to the limit as \(\mathsf {T}\rightarrow \infty \).
By confidence bound at level \(1-\alpha \), we mean a bound under which the distance \(d_{\text {trans}}(S_N,S)\) stays with probability (at least) \(1-\alpha \). We gather some typical examples in Table 4.
For instance in Eq. (36), to compute the constant \(C(x)=\sqrt{2x}+\sqrt{\frac{2}{\pi }}(1+\log 2)\), take \(x\) at least \(\log 100\) to obtain a 99 % confidence limit and note that \(C(\log 100)\simeq 4.386\). For a 95 % confidence limit, take \(x\) at least \(\log 20\) and note that \(C(\log 20)\simeq 3.799\). And for a 90 % confidence limit, take \(x\) at least \(\log 10\) and note that \(C(\log 10)\simeq 3.497\).
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Heinrich, P., Gonzalez Pisfil, M., Kahn, J. et al. Implementation of Transportation Distance for Analyzing FLIM and FRET Experiments. Bull Math Biol 76, 2596–2626 (2014). https://doi.org/10.1007/s11538-014-0025-9
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DOI: https://doi.org/10.1007/s11538-014-0025-9