Outreach

 Hayde O. Hernandez Aviña, Monica Ramirez Vazquez, Jose  Fabian Villa Manriquez y Paul Hernandez Herrera,  "Nuevas herramientas para ver lo imperceptible", Nuevos Dialogos, Numero 2,  pp 49-52, 2023. PDF  

Journals

A. Bribiesca-Sánchez, A. Guzmán, F. Montoya,  D. Díaz-Guerrero, H. O. Hernández, P. Hernández-Herrera, A. Darszon, G. Corkidi, E. Bribiesca, " A Three-Dimensional Extension of the Slope Chain Code: Analyzing the Tortuosity of the Flagellar Beat of Human Sperm", 2024, (Under review) https://www.researchsquare.com/article/rs-3694554/latest.pdf  

Haydee O. Hernandez, Fernando Montoya, Paúl Hernández-Herrera, Dan S. Díaz-Guerrero, Jimena Olveres, Alberto Darszon, Boris Escalante-Ramirez, Gabriel Corkidi, "Feature-Based 3D+t Descriptors of Hyperactivated Human Sperm Beat Patterns", 2024, https://doi.org/10.1016/j.heliyon.2024.e26645 , BioRxiv

Paúl Hernández-Herrera, Victor Abonza, Jair Sánchez-Contreras, Alberto Darszon, Adan Guerrero. (2023), "Deep Learning Based-Classification and Segmentation of Sperm head and flagellum for Image-Based Flow Cytometry", Computación y Sistemas, 27(4)  https://www.cys.cic.ipn.mx/ojs/index.php/CyS/article/view/4772/3617 

G. Corkidi, F. Montoya, A.L. González-Mota, P- Hernández-Herrera,  N.C. Bruce, H. Bloomfield-Gadelha, A. Darszon, (2023). “The human sperm  rotates with a conserved direction during free swimming in four dimensions”, Journal of Cell Science, 136(22) https://doi.org/10.1242/jcs.261306
 BioRxiv,  

S. G. de León-Rodríguez, P. Hernández-Herrera, C. Aguilar-Flores, V. Perez-Koldenkova, A. Guerrero, A. Mantilla, E.M. Fuentes-Panana, C. Wood, L. Bonifaz, “A machine learning workflow of multiplexed immunofluorescence images to interrogate activator and tolerogenic profiles of conventional type 1 dendritic cells infiltrating melanomas of disease-free and metastatic patients”, Journal of Oncology, vol. 2022, Article ID 9775736, 20 pages, 2022, https://www.hindawi.com/journals/jo/2022/9775736/ 

 A. Alva, E. Brito-Alarcón, A. Linares, E. Torres-García, Hayde O. Hernández, R. Pinto-Cámara, D. Martinez, P. Hernández-Herrera, R. D’Antuono, C. Wood, A. Guerrero, “Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start”, Journal of Microscopy (2022), https://doi.org/10.1111/jmi.13135   
bioRxiv version 

 P. Hernández-Herrera, Y. Ugartechea-Chirino, H. Torres-Martinez, A.V. Arzola, J.E. Chairez-Veloz, B. García-Ponce, M. de la Paz-Sanchez, A. Garay-Arroyo, E.A. Álverez-Buylla, J. Dubrovsky, G. Corkidi, “Live Plant Cell Tracking: Fiji plugin to analyze cell proliferation dynamics and understanding morphogenesis”, Plant Physiology (2022), vol. 188, no 2 p. 846-860, https://doi.org/10.1093/plphys/kiab530

 E. Mata-Martínez, C. Sánchez-Cárdenas, J. C. Chávez, A. Guerrero, C. L. Treviño, G. Corkidi, F. Montoya, P. Hernández-Herrera,  M. G. Buffone, P. A. Balestrini, A. Darszon, "Role of calcium oscillations in sperm physiology." Biosystems(2021): 104524. https://doi.org/10.1016/j.biosystems.2021.104524 

G. Corkidi, P. Hernandez-Herrera, F. Montoya, JM, Hermes Gadelha and A. Darszon “Long-term segmentation-free assessment of head-flagellum movement and intracellular calcium in swimming human sperm”,Journal of Cell Science, no. 134(3):jcs250654, 2021. https://doi.org/10.1242/jcs.250654
bioRxiv version 

 H.H. Torres-Martinez, P. Hernandez-Herrera, G. Corkidi and J. Dubrovsky, “From one cell to many: Morphogenetic field of lateral root founder cells in Arabidopsis thaliana is built by gradual recruitment”, Proceedings of the National Academy of Sciences 117, no. 34 (2020): 20943-20949. https://doi.org/10.1073/pnas.2006387117

 A. Bibriesca, F. Montoya, P. Hernandez-Herrera, E. Ramos and G. Corkidi, “Device for experimental characterization of the 4D flow inside an evaporating sessile water droplet”, Review of Scientific Instruments, 9, 016101, 2020. https://doi.org/10.1063/1.5126112

 P. Hernandez-Herrera, F. Montoya, JM Rendón-Mancha, A. Darszon and G. Corkidi, “3D+t Human Sperm Flagellum Tracing in low SNR Fluorescence Images”, IEEE Transactions on Medical Imaging, 37(10), 2236-2247, 2018.  https://doi.org/10.1109/TMI.2018.2840047

 G. Corkidi, F. Montoya, P. Hernandez-Herrera, Wa. Ríos-Herrera, MF Müller, CL Treviño and A Darszon, “Are there intracellular Ca2+ oscillations correlated with flagellar beating in human sperm? A three vs. two-dimensional analysis”, MHR: Basic science of reproductive medicine, 23(9), 583-593, 2017. https://doi.org/10.1093/molehr/gax039 

 P.K. Singh, P.  Hernandez-Herrera, D. Labate and M. Papadakis, “Automated 3-D detection of dendritic spines from in vivo two-photon image stacks”, Neuroinformatics, 15(4), 303-319, 2017. https://doi.org/10.1007/s12021-017-9332-2

 P. Hernandez-Herrera, M. Papadakis and I. A. Kakadiaris, “Multi-Scale Segmentation of Neurons Based on One-Class Classification”, Journal of Neuroscience Methods, 266, 94-106, 2016. https://doi.org/10.1016/j.jneumeth.2016.03.019

A. Santamaria-Pang, P. Hernandez-Herrera, M. Papadakis, P. Saggau and I. A. Kakadiaris, “Automatic Morphological Reconstruction of Neurons from Multiphoton and Confocal Microscopy Images Using 3D Tubular Models”, Neuroinformatics, 13(3), 297-320, 2015. https://doi.org/10.1007/s12021-014-9253-2 

Book Chapter 

 P. Hernandez-Herrera, D. Jimenez, I. A. Kakadiaris, A. Koutsogiannis, D. Labate, F. Laezza and E. Papadakis (2013), "A Harmonic Analysis View on Neuroscience Imaging", in: J. Benedetto, T. Andrews, R. Balan, W. Czaja, K. (eds) Excursion in Harmonic Analysis, Volume 2, Applied and Numerical Harmonic Analysis, Birkhäuser Boston, pp 423-450.  https://doi.org/10.1007/978-0-8176-8379-5_21 

Conference 

Díaz-Guerrero, D.S., Montoya, F., Hernández, H.O., Hernández-Herrera, P., Darszon, A., Corkidi, G. (2024). Computation of Human-Sperm Local Flagellar Instantaneous Velocity. In: Flores Cuautle, J.d.J.A., et al. XLVI Mexican Conference on Biomedical Engineering. CNIB 2023. IFMBE Proceedings, vol 96. Springer, Cham. https://doi.org/10.1007/978-3-031-46933-6_7 

H.O.  Hernández-Aviña, P.  Hernández-Herrera,  F. Montoya, J. Olveres, H. Bloomfield-Gadelha, A. Darszon, B. Escalante-Ramirez, G. Corkidi, “3D feature-based descriptor for unsupervised flagellar human sperm beat classification”, in Proc. International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, United Kingdom, 11-15 July 2022. https://doi.org/10.1109/EMBC48229.2022.9871419 

 A. Bibriesca, F. Montoya, A.L. Cota-González, P. Hernandez-Herrera, E. Ramos and G. Corkidi, “Artifacts Generated by the 3D rotation of a freely-swimming human sperm in the measurement of Ca2+”, Memorias del Congreso Nacional de Ingeniería Biomédica, Puerto Vallarta, México, Octubre, 2022, pp. 1-7. https://doi.org/10.1007/978-3-031-18256-3_39 

 A Bibriesca, F. Montoya, P. Hernandez-Herrera, E Ramos and G. Corkidi, “Análisis de la dinámica tridimensional de evaporación de gotas sésiles de interés biomédico”, Memorias del Congreso Nacional de Ingeniería Biomédica, Guadalajara, México, Noviembre, 2021, pp. 69-72. http://dx.doi.org/10.24254/CNIB.21.5 

 A. Bibriesca, F. Montoya, P. Hernandez-Herrera, E. Ramos and G. Corkidi, “Metodología para el análisis 3D de la evaporación y sedimentación de una gota de agua”, SOMI XXXIV Congreso de Instrumentación, Morelia, México, Oct 16-18, 2019, pp. 1-7. ISSN 2395-8499 PDF file

 A. Bibriesca, F. Montoya, P. Hernandez-Herrera, E. Ramos and G. Corkidi, “Sistema de Microscopía tridimensional para muestreo rápido y ‘time lapse’ simultáneamente”, SOMI XXXIII Congreso de Instrumentación, Guerrero, México, Oct 29-31, 2018, pp. 1-7. ISSN 2395-8499 PDF file 

 Gabriel Corkidi, José Montoya, Saúl Piedra, Andrés Bribiesca, Paúl Hernández-Herrera and Eduardo Ramos. “Observations of three dimensional flow inside an evaporating drops”, Proceedings of the 19th International Symposium on Applications of Laser and Imaging Techniques to Fluid Mechanics, Lisboa, Portugal, 16-19 July 2018, pp. 1157-1162.  https://www.lisbonsimposia.org/blank-cjg9

 P. Hernandez-Herrera, F. Montoya, J.M. Rendon-Mancha, A. Darszon and G. Corkidi, “Sperm flagellum center-line tracing in Fluorescense 3D+t low SNR Stacks using an iterative minimal path method”, in Proc. International Conference on Image Analysis and Recognition, Montreal, Canada, Jul. 5-7, 2017, pp. 437-445. https://doi.org/10.1007/978-3-319-59876-5_48 

 A. Bibriesca, F Montoya, P. Hernandez-Herrera, E. Ramos and G. Corkidi, “Instrumentación y Algoritmos para el Análisis de la Dinámica Tridimensional de Evaporación de Gotas Sésiles de Agua”, SOMI XXXII Congreso de Instrumentación, Guerrero, México, Oct 25-27, 2017, pp. 1-7. ISSN 2395-8499  PDF file 

H. Ehrlich, F. Montoya, P. Hernandez-Herrera, A. Darszon and G. Corkidi, “Análisis de Métricas Sobre el Flagelo de Espermatozoides de Humano en 3D para su Clasificación  entre Activados e Hiperactivados”, Memorias del Congreso Nacional de Ingeniería Biomédica, Nuevo León, México, Nov 1-4, 2017, pp. 182-185. https://dx.doi.org/10.24254/CNIB.17.29

 P. Hernandez-Herrera, M. Papadakis and I. A. Kakadiaris, “Segmentation of Neurons Based On One-Class Classification”, in Proc. IEEE International Symposium of Biomedical Imaging, Beijing, China, Apr 28- May 2, 2014, pp. 1316-1319. https://doi.org/10.1109/ISBI.2014.6868119