Deep learning for nanofluidic scattering microscopy
Typ
Examensarbete för masterexamen
Program
Publicerad
2021
Författare
Sjösten, Gustaf
Modellbyggare
Tidskriftstitel
ISSN
Volymtitel
Utgivare
Sammanfattning
A novel technique for label-free, real-time characterization of single biomolecules
called Nanofluidic Scatter Microscopy (NSM) has recently been developed by a the
Langhammer research group at Chalmers. We have created a machine learning (ML)
framework consisting of deep convolutional neural networks such as U-nets, FCNNs,
and YOLO in order to characterize single biomolecules through kymographs collected
through NSM, as an alternative approach to a standard data analysis method
(SA). As a laser irradiates visible light onto single biomolecules freely diffusing in
solution inside nanofluidic channels, the biomolecule and the nanochannel scatter
light coherently into the collection optics, such that the nanochannels improve the
optical contrast of the imaged biomolecules by several orders of magnitude. A video
of the total scattering intensity is then recorded with a high frame rate camera
(capturing 200 fps) in order to capture the movement of the molecules as well as
the optical contrast of the biomolecules with respect to the nanochannel. From the
movement of one single biomolecule, it is possible to predict its diffusion constant,
which can then be used to infer the hydrodynamic radius of the biomolecule. Additionally,
the predicted optical contrast of one single biomolecule can in turn be used
to infer its molecular weight. From the combination of hydrodynamic radius and
molecular weight, information about the conformal state of single biomolecules can
be inferred. In this thesis, we show that the ML approach yields results comparable
to the SA which was developed independently of the ML technique for biomolecules
in the weight span 66-669 kDa, and we also show that the ML technique is superior
to the SA in other regards, such as computational speed and potential to characterize
smaller molecules. The results of the data analysis performed with the ML
framework will also make an appearance in the first paper on the NSM technique
which has been submitted for publication and is currently under review.
Beskrivning
Ämne/nyckelord
data analysis , machine learning , deep convolutional neural networks , nanofluidic scattering spectroscopy , biomolecules , physical chemistry , dark-field microscopy