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Computer vision with deep learning is emerging as a significant approach for non-invasive and non-destructive plant phenotyping. Spikes are the reproductive organs of wheat plants. Detection and counting of spikes considered the grain-bearing organ have great importance in the phenomics study of large sets of germplasms. In the present study, we developed an online platform, “Web-SpikeSegNet,” based on a deep-learning framework for spike detection and counting from the wheat plant’s visual images. The architecture of the Web-SpikeSegNet consists of 2 layers. First Layer, Client-Side Interface Layer, deals with end user’s requests and corresponding responses management. In contrast, the second layer, Server Side Application Layer, consists of a spike detection and counting module. The backbone of the spike detection module comprises of deep encoder-decoder network with hourglass network for spike segmentation. The Spike counting module implements the “Analyze Particle” function of imageJ to count the number of spikes. For evaluating the performance of Web-SpikeSegNet, we acquired the wheat plant’s visual images, and the satisfactory segmentation performances were obtained as Type I error 0.00159, Type II error 0.0586, Accuracy 99.65%, Precision 99.59% and F₁ score 99.65%. As spike detection and counting in wheat phenotyping are closely related to the yield, Web-SpikeSegNet is a significant step forward in the field of wheat phenotyping and will be very useful to the researchers and students working in the domain.