Segmentation, tracking, and sub-cellular feature extraction in 3D time-lapse images

[1]  Anne L. Martel,et al.  Cell segmentation for immunofluorescence multiplexed images using two-stage domain adaptation and weakly labeled data for pre-training , 2022, Scientific Reports.

[2]  M. Kowalska,et al.  Management of validation of HPLC method for determination of acetylsalicylic acid impurities in a new pharmaceutical product , 2022, Scientific Reports.

[3]  J. Turner,et al.  Real-time conversion of tissue-scale mechanical forces into an interdigitated growth pattern , 2021, Nature Plants.

[4]  Marius Pachitariu,et al.  Cellpose: a generalist algorithm for cellular segmentation , 2020, Nature Methods.

[5]  B. S. Manjunath,et al.  Semi Supervised Segmentation And Graph-Based Tracking Of 3d Nuclei In Time-Lapse Microscopy , 2020, 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI).

[6]  Peng Gao,et al.  Joint Multi-frame Detection and Segmentation for Multi-cell Tracking , 2019, ICIG.

[7]  Minh-Triet Tran,et al.  Enhanced Rotation-Equivariant U-Net for Nuclear Segmentation , 2019, 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).

[8]  Kazuhiro Hotta,et al.  Cell Image Segmentation by Integrating Pix2pixs for Each Class , 2019, 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).

[9]  Peter Bajcsy,et al.  Cell Image Segmentation Using Generative Adversarial Networks, Transfer Learning, and Augmentations , 2019, 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).

[10]  B. S. Manjunath,et al.  BisQue for 3D Materials Science in the Cloud: Microstructure–Property Linkages , 2019, Integrating Materials and Manufacturing Innovation.

[11]  B. S. Manjunath,et al.  Accurate 3D Cell Segmentation Using Deep Features and CRF Refinement , 2019, 2019 IEEE International Conference on Image Processing (ICIP).

[12]  S. Braybrook,et al.  Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape , 2018, bioRxiv.

[13]  Vijay Kumar,et al.  Cell Tracking with Deep Learning and the Viterbi Algorithm , 2018, 2018 International Conference on Manipulation, Automation and Robotics at Small Scales (MARSS).

[14]  Enrico Scarpella,et al.  Reassessing the Roles of PIN Proteins and Anticlinal Microtubules during Pavement Cell Morphogenesis1[OPEN] , 2017, Plant Physiology.

[15]  Andreas Bartschat,et al.  Cell segmentation in 3D confocal images using supervoxel merge-forests with CNN-based hypothesis selection , 2017, 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018).

[16]  Nathalie Harder,et al.  An Objective Comparison of Cell Tracking Algorithms , 2017, Nature Methods.

[17]  Birgit Möller,et al.  PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics1[OPEN] , 2017, Plant Physiology.

[18]  Juho Kannala,et al.  Cell Tracking via Proposal Generation and Selection , 2017, ArXiv.

[19]  Henrik Jönsson,et al.  Research data supporting Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche , 2017 .

[20]  Tzu-Ching Wu,et al.  LobeFinder: A Convex Hull-Based Method for Quantitative Boundary Analyses of Lobed Plant Cells1[OPEN] , 2016, Plant Physiology.

[21]  B. S. Manjunath,et al.  CellECT: cell evolution capturing tool , 2016, BMC Bioinformatics.

[22]  Philipp J. Keller,et al.  Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos. , 2016, Developmental cell.

[23]  Joakim Jalden,et al.  Global Linking of Cell Tracks Using the Viterbi Algorithm , 2015, IEEE Transactions on Medical Imaging.

[24]  Nathalie Harder,et al.  A benchmark for comparison of cell tracking algorithms , 2014, Bioinform..

[25]  Kishore Mosaliganti,et al.  ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes , 2012, PLoS Comput. Biol..

[26]  Haim Kaplan,et al.  Computing the Discrete Fréchet Distance in Subquadratic Time , 2012, SIAM J. Comput..

[27]  Vladlen Koltun,et al.  Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials , 2011, NIPS.

[28]  G. Malandain,et al.  Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution , 2010, Nature Methods.

[29]  Xin-Guang Zhu,et al.  Improving photosynthetic efficiency for greater yield. , 2010, Annual review of plant biology.

[30]  Ambuj K. Singh,et al.  Bisque: a platform for bioimage analysis and management , 2009, Bioinform..

[31]  Kai-Kuang Ma,et al.  Scale-Space Behavior of Planar-Curve Corners , 2009, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[32]  Joanne Chory,et al.  The epidermis both drives and restricts plant shoot growth , 2007, Nature.