Efficient parallel Levenberg-Marquardt model fitting towards real-time automated parametric imaging microscopy

Real-time open-source FLIM analysis

Fluorescence lifetime imaging microscopy (FLIM) provides valuable quantitative insights into fluorophores' chemical microenvironment. Due to long computation times and the lack of accessible, open-source real-time analysis toolkits, traditional analysis of FLIM data, particularly with the widely used time-correlated single-photon counting (TCSPC) approach, typically occurs after acquisition. As a result, uncertainties about the quality of FLIM data persist even after collection, frequently necessitating the extension of imaging sessions. Unfortunately, prolonged sessions not only risk missing important biological events but also cause photobleaching and photodamage. We present the first open-source program designed for real-time FLIM analysis during specimen scanning to address these challenges. Our approach combines acquisition with real-time computational and visualization capabilities, allowing us to assess FLIM data quality on the fly. Our open-source real-time FLIM viewer, integrated as a Napari plugin, displays phasor analysis and rapid lifetime determination (RLD) results computed from real-time data transmitted by acquisition software such as the open-source Micro-Manager-based OpenScan package. Our method facilitates early identification of FLIM signatures and data quality assessment by providing preliminary analysis during acquisition. This not only speeds up the imaging process, but it is especially useful when imaging sensitive live biological samples.

Multiplex-multiphoton microscopy and computational strategy for biomedical imaging

We demonstrate the benefit of a novel laser strategy in multiphoton microscopy (MPM). The cheap, simple, and turn-key supercontinuum laser system with its spectral shaping module, constitutes an ideal approach for the one-shot microscopic imaging of many fluorophores without modification of the excitation parameters: central wavelength, spectral bandwidth, and average power. The polyvalence of the resulting multiplex-multiphoton microscopy (M-MPM) device is illustrated by images of many biomedical models from several origins (biological, medical, or vegetal), generated while keeping constant the spectral parameters of excitation. The resolution of the M-MPM device is quantified by a procedure of point-spread-function (PSF) assessment led by an original, robust, and reliable computational approach FIGARO. The estimated values for the PSF width for our M-MPM system are shown to be comparable to standard values found in optical microscopy. The simplification of the excitation system constitutes a significant instrumental progress in biomedical MPM, paving the way to the imaging of many fluorophores with a single shot of excitation without any modification of the lighting device. RESEARCH HIGHLIGHTS: A new solution of multiplex-multiphoton microscopy device is shown, resting on a supercontinuum laser. The one-shot excitation device has imaged biomedical and vegetal models. Our original computational strategy measures usual microscopy resolution.

Characterization of synovial fluid from periprosthetic infection in revision total joint arthroplasty by single-molecule microscopy

Periprosthetic joint infection is among the most common and severe complications in total joint arthroplasty. Today, a combination of different methods is used for diagnosis because no single method with sufficient sensitivity and specificity is available. In this study, we explored the usability of single-molecule microscopy to characterize synovial fluid samples from periprosthetic joint infections. Patients (n = 27) that needed revision arthroplasty underwent the routine diagnostic procedures for periprosthetic joint infection of the University Hospital in Bonn. Additionally, the diffusion rate of two probes, dextran and hyaluronan, was measured in small volumes of periprosthetic synovial fluid samples using single-molecule microscopy. To evaluate the suitability of single-molecule microscopy to detect PJI the AUC for both markers was calculated. The diffusion rate of hyaluronan in periprosthetic synovial fluid from patients with septic loosening was faster than in samples from patients with aseptic loosening. Single-molecule microscopy showed excellent diagnostic performance, with an area under the receiver operating characteristic curve of 0.93, and allowed the detection of periprosthetic joint infection in patients that would be challenging to diagnose with current methods. For the first time, single-molecule microscopy was used to detect periprosthetic joint infection. Our results are encouraging to study the value of single-molecule microscopy in a larger patient cohort. The speed and accuracy of single-molecule microscopy can be used to further characterize synovial fluid, potentially allowing intraoperative diagnosis of periprosthetic joint infections in the future.

Estimation of Biological Parameters of Cutaneous Ulcers Caused by Leishmaniasis in an Animal Model Using Diffuse Reflectance Spectroscopy

Cutaneous leishmaniasis (CL) is a neglected tropical disease that requires novel tools for its understanding, diagnosis, and treatment follow-up. In the cases of other cutaneous pathologies, such as cancer or cutaneous ulcers due to diabetes, optical diffuse reflectance-based tools and methods are widely used for the investigation of those illnesses. These types of tools and methods offer the possibility to develop portable diagnosis and treatment follow-up systems. In this article, we propose the use of a three-layer diffuse reflectance model for the study of the formation of cutaneous ulcers caused by CL. The proposed model together with an inverse-modeling procedure were used in the evaluation of diffuse-reflectance spectral signatures acquired from cutaneous ulcers formed in the dorsal area of 21 golden hamsters inoculated with Leishmanisis braziliensis. As result, the quantification of the model’s variables related to the main biological parameters of skin were obtained, such as: diameter and volumetric fraction of keratinocytes, collagen; volumetric fraction of hemoglobin, and oxygen saturation. Those parameters show statistically significant differences among the different stages of the CL ulcer formation. We found that these differences are coherent with histopathological manifestations reported in the literature for the main phases of CL formation.

A Novel method to generate on-board 4D MRI using prior 4D MRI and on-board kV projections from a conventional LINAC for target localization in liver SBRT

PURPOSE

On-board MRI can provide superb soft tissue contrast for improving liver SBRT localization. However, the availability of on-board MRI in clinics is extremely limited. On the contrary, on-board kV imaging systems are widely available on radiotherapy machines, but its capability to localize tumors in soft tissue is limited due to its poor soft tissue contrast. This study aims to explore the feasibility of using an on-board kV imaging system and patient prior knowledge to generate on-board four-dimensional (4D)-MRI for target localization in liver SBRT.

METHODS

Prior 4D MRI volumes were separated into end of expiration (EOE) phase (MRI_prior ) and all other phases. MRI_prior was used to generate a synthetic CT at EOE phase (sCT_prior ). On-board 4D MRI at each respiratory phase was considered a deformation of MRI_prior . The deformation field map (DFM) was estimated by matching DRRs of the deformed sCT_prior to on-board kV projections using a motion modeling and free-form deformation optimization algorithm. The on-board 4D MRI method was evaluated using both XCAT simulation and real patient data. The accuracy of the estimated on-board 4D MRI was quantitatively evaluated using Volume Percent Difference (VPD), Volume Dice Coefficient (VDC), and Center of Mass Shift (COMS). Effects of scan angle and number of projections were also evaluated.

RESULTS

In the XCAT study, VPD/VDC/COMS among all XCAT scenarios were 10.16 ± 1.31%/0.95 ± 0.01/0.88 ± 0.15 mm using orthogonal-view 30° scan angles with 102 projections. The on-board 4D MRI method was robust against the various scan angles and projection numbers evaluated. In the patient study, estimated on-board 4D MRI was generated successfully when compared to the "reference on-board 4D MRI" for the liver patient case.

CONCLUSIONS

A method was developed to generate on-board 4D MRI using prior 4D MRI and on-board limited kV projections. Preliminary results demonstrated the potential for MRI-based image guidance for liver SBRT using only a kV imaging system on a conventional LINAC.

Gpufit: An open-source toolkit for GPU-accelerated curve fitting

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.

A novel profile/view ordering with a non-convex star shutter for high-resolution 3D volumetric T1 mapping under multiple breath-holds

PURPOSE

To examine a novel non-convex star ordering/shutter for reducing the number of breath-holds in cardiac three-dimensional (3D) T₁ Mapping MRI with multiple breath-holds.

METHODS

A novel ordering, Non-Convex Star (NCS) was designed to acquire 3D volumes in a modified look-locker inversion recovery (MOLLI) T₁ mapping sequence to provide more spatial resolution and coverage in fewer breath-holds. The proposed 3D-MOLLI approach using NCS was first validated in two phantoms using artifact power (AP) measurement against the fully sampled phantom. This was followed by an in vivo study in seven swine, in which the T₁ values of the left ventricular (LV) myocardium divided into the American Heart Association (AHA) 16-segment model was compared against the reference multislice two-dimensional (2D) clinical reference and 3D volume without NCS breath-hold reduction.

RESULTS

NCS breath-hold reduction yielded less AP compared with the matched SENSE accelerated phantom volume (P < 0.0005), and was shown to be optimal at 25% fewer breath-holds. Calculated T₁ values from 3D in vivo volumes with/without NCS were comparable in all AHA segments (P = NS), whereas 3D-NCS yielded significantly higher T₁ values than 2D at midslice of the LV myocardium in each AHA segment (P < 0.05).

CONCLUSION

We successfully demonstrate the feasibility of the NCS approach for a 3D T₁ mapping acquisition requiring fewer breath-holds. Magn Reson Med 77:2215-2224, 2017. © 2016 International Society for Magnetic Resonance in Medicine.