NeuriTES. Monitoring neurite changes through transfer entropy and semantic segmentation in bright-field time-lapse microscopy

Summary One of the most challenging frontiers in biological systems understanding is fluorescent label-free imaging. We present here the NeuriTES platform that revisits the standard paradigms of video analysis to detect unlabeled objects and adapt to the dynamic evolution of the phenomenon under observation. Object segmentation is reformulated using robust algorithms to assure regular cell detection and transfer entropy measures are used to study the inter-relationship among the parameters related to the evolving system. We applied the NeuriTES platform to the automatic analysis of neurites degeneration in presence of amyotrophic lateral sclerosis (ALS) and to the study of the effects of a chemotherapy drug on living prostate cancer cells (PC3) cultures. Control cells have been considered in both the two cases study. Accuracy values of 93% and of 92% are achieved, respectively. NeuriTES not only represents a tool for investigation in fluorescent label-free images but demonstrates to be adaptable to individual needs.

[1]  A. Efrat,et al.  NeuronMetrics: Software for semi-automated processing of cultured neuron images , 2007, Brain Research.

[2]  P. Caroni,et al.  Early and Selective Loss of Neuromuscular Synapse Subtypes with Low Sprouting Competence in Motoneuron Diseases , 2000, The Journal of Neuroscience.

[3]  Shinn-Ying Ho,et al.  NeurphologyJ: An automatic neuronal morphology quantification method and its application in pharmacological discovery , 2011, BMC Bioinformatics.

[4]  David M. W. Powers,et al.  Evaluation: from precision, recall and F-measure to ROC, informedness, markedness and correlation , 2011, ArXiv.

[5]  C. Shaw,et al.  Familial amyotrophic lateral sclerosis-linked SOD1 mutants perturb fast axonal transport to reduce axonal mitochondria content. , 2007, Human molecular genetics.

[6]  J. Weiss,et al.  Motor Neurons Are Selectively Vulnerable to AMPA/Kainate Receptor-Mediated Injury In Vitro , 1996, The Journal of Neuroscience.

[7]  G. Bernardi,et al.  Cu/Zn-superoxide dismutase (GLY93→ALA) mutation alters AMPA receptor subunit expression and function and potentiates kainate-mediated toxicity in motor neurons in culture , 2004, Neurobiology of Disease.

[8]  A. Ossinger,et al.  A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning , 2019, Journal of Neuroscience Methods.

[9]  N. Shneider,et al.  Mutant TDP-43 Causes Early-Stage Dose-Dependent Motor Neuron Degeneration in a TARDBP Knockin Mouse Model of ALS. , 2019, Cell reports.

[10]  Markus W. Covert,et al.  Techniques for Studying Decoding of Single Cell Dynamics , 2019, Front. Immunol..

[11]  J. Glass,et al.  Amyotrophic lateral sclerosis is a distal axonopathy: evidence in mice and man , 2004, Experimental Neurology.

[12]  Judea Pearl,et al.  The recovery of causal poly-trees from statistical data , 1987, Int. J. Approx. Reason..

[13]  S. Duguez,et al.  Molecular and Cellular Mechanisms Affected in ALS , 2020, Journal of personalized medicine.

[14]  C. Elizabeth Caldon,et al.  Label free, quantitative single-cell fate tracking of time-lapse movies , 2019, MethodsX.

[15]  Lluís Jover,et al.  Estimating the Generalized Concordance Correlation Coefficient through Variance Components , 2003, Biometrics.

[16]  Schreiber,et al.  Measuring information transfer , 2000, Physical review letters.

[17]  Matthew A. White,et al.  Sarm1 deletion suppresses TDP-43-linked motor neuron degeneration and cortical spine loss , 2019, Acta Neuropathologica Communications.

[18]  K. D. De Vos,et al.  Amyotrophic lateral sclerosis-associated mutant SOD1 inhibits anterograde axonal transport of mitochondria by reducing Miro1 levels , 2017, Human molecular genetics.

[19]  Sergei Vassilvitskii,et al.  k-means++: the advantages of careful seeding , 2007, SODA '07.

[20]  M. Bickle,et al.  Knocking out C9ORF72 Exacerbates Axonal Trafficking Defects Associated with Hexanucleotide Repeat Expansion and Reduces Levels of Heat Shock Proteins , 2020, Stem cell reports.

[21]  A. Hyman,et al.  Impaired DNA damage response signaling by FUS-NLS mutations leads to neurodegeneration and FUS aggregate formation , 2018, Nature Communications.

[22]  Xiaobo Zhou,et al.  Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assays , 2007, NeuroImage.

[23]  J. Walker‐Daniels,et al.  Live Cell Imaging Methods Review , 2012 .

[24]  W. Robberecht,et al.  AMPA Receptor Calcium Permeability, GluR2 Expression, and Selective Motoneuron Vulnerability , 2000, The Journal of Neuroscience.

[25]  K. Thorn.  A quick guide to light microscopy in cell biology , 2016, Molecular biology of the cell.

[26]  Elizabeth A. Specht,et al.  A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging. , 2017, Annual review of physiology.

[27]  Jian Sun,et al.  Deep Residual Learning for Image Recognition , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[28]  Peter J O'Toole,et al.  Characterising live cell behaviour: Traditional label-free and quantitative phase imaging approaches. , 2017, The international journal of biochemistry & cell biology.

[29]  N. Senthilkumaran,et al.  Image Segmentation - A Survey of Soft Computing Approaches , 2009, 2009 International Conference on Advances in Recent Technologies in Communication and Computing.

[30]  Tom Fawcett,et al.  An introduction to ROC analysis , 2006, Pattern Recognit. Lett..

[31]  M. Pool,et al.  NeuriteTracer: A novel ImageJ plugin for automated quantification of neurite outgrowth , 2008, Journal of Neuroscience Methods.

[32]  A. Torres-Espín,et al.  Neurite-J: An Image-J plug-in for axonal growth analysis in organotypic cultures , 2014, Journal of Neuroscience Methods.

[33]  D. Cleveland,et al.  ALS: A Disease of Motor Neurons and Their Nonneuronal Neighbors , 2006, Neuron.

[34]  Luca Faes,et al.  MuTE: A MATLAB Toolbox to Compare Established and Novel Estimators of the Multivariate Transfer Entropy , 2014, PloS one.

[35]  Arnold Kamis,et al.  A Review of Three Directed Acyclic Graphs Software Packages , 2006 .

[36]  Yassine Ruichek,et al.  Survey on semantic segmentation using deep learning techniques , 2019, Neurocomputing.

[37]  Li Cheng,et al.  NeuronCyto II: An automatic and quantitative solution for crossover neural cells in high throughput screening , 2016, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[38]  E. Melamed,et al.  The “Dying-Back” Phenomenon of Motor Neurons in ALS , 2011, Journal of Molecular Neuroscience.

[39]  Athanasios Papoulis,et al.  Probability, Random Variables and Stochastic Processes , 1965 .

[40]  M. Gurney,et al.  Motor neuron degeneration in mice that express a human Cu,Zn superoxide dismutase mutation. , 1994, Science.

[41]  Zian Fanti,et al.  Neurongrowth, a software for automatic quantification of neurite and filopodial dynamics from time‐lapse sequences of digital images , 2011, Developmental neurobiology.

[42]  George Papandreou,et al.  Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation , 2018, ECCV.

[43]  C. Blizzard,et al.  Axonal degeneration, distal collateral branching and neuromuscular junction architecture alterations occur prior to symptom onset in the SOD1G93A mouse model of amyotrophic lateral sclerosis , 2016, Journal of Chemical Neuroanatomy.

[44]  Tony J Collins,et al.  ImageJ for microscopy. , 2007, BioTechniques.

[45]  Arianna Mencattini,et al.  Learning Cancer-Related Drug Efficacy Exploiting Consensus in Coordinated Motility Within Cell Clusters , 2019, IEEE Transactions on Biomedical Engineering.

[46]  Emanuele Trucco,et al.  Computer and Robot Vision , 1995 .

[47]  J. Pearl.  Causality: Models, Reasoning and Inference , 2000 .

[48]  E Meijering,et al.  Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[49]  Pico Caroni,et al.  Selective vulnerability and pruning of phasic motoneuron axons in motoneuron disease alleviated by CNTF , 2006, Nature Neuroscience.