Efficient Cochlear Implant (CI) surgery requires prior knowledge of the cochlea’s size and its characteristics. This information helps to select suitable implants for different patients. Registered and fused images helps doctors by providing more informative image that takes advantages of different modalities. The cochlea’s small size and complex structure, in addition to the different resolutions and head positions during imaging, reveals a big challenge for the automated registration of the different image modalities. To obtain an automatic measurement of the cochlea length and the volume size, a segmentation method of cochlea medical images is needed. The goal of this dissertation is to introduce new practical and automatic algorithms for the human cochlea multi-modal 3D image registration, fusion, segmentation and analysis. Two novel methods for automatic cochlea image registration (ACIR) and automatic cochlea analysis (ACA) are introduced. The proposed methods crop the input images to the cochlea part and then align the cropped images to obtain the optimal transformation. After that, this transformation is used to align the original images. ACIR and ACA use Mattes mutual information as similarity metric, the adaptive stochastic gradient descent (ASGD) or the stochastic limited memory Broyden–Fletcher–Goldfarb–Shanno (s-LBFGS) optimizer to estimate the parameters of 3D rigid transform. The second stage of nonrigid registration estimates B-spline coefficients that are used in an atlas-model-based segmentation to extract cochlea scalae and the relative measurements of the input image. The image which has segmentation is aligned to the input image to obtain the non-rigid transformation. After that the segmentation of the first image, in addition to point-models are transformed to the input image. The detailed transformed segmentation provides the scala volume size. Using the transformed point-models, the A-value, the central scala lengths, the lateral and the organ of corti scala tympani lengths are computed. The methods have been tested using clinical 3D images of total 67 patients: from Germany (41 patients) and Egypt (26 patients). The atients are of different ages and gender. The number of images used in the experiments is 217, which are multi-modal 3D clinical images from CT, CBCT, and MRI scanners. The proposed methods are compared to the state of the arts ptimizers related medical image registration methods e.g. fast adaptive stochastic gradient descent (FASGD) and efficient preconditioned tochastic gradient descent (EPSGD). The comparison used the root mean squared distance (RMSE) between the ground truth landmarks and the resulted landmarks. The landmarks are located manually by two experts to represent the round window and the top of the cochlea. After obtaining the transformation using ACIR, the landmarks of the moving image are transformed using the resulted transformation and RMSE of the transformed landmarks, and at the same time the fixed image landmarks are computed. I also used the active length of the cochlea implant electrodes to compute the error aroused by the image artifact, and I found out an error ranged from 0.5 mm to 1.12 mm. ACIR method’s RMSE average was 0.36 mm with a standard deviation (SD) of 0.17 mm. The total time average required for registration of an image pair using ACIR was 4.62 seconds with SD of 1.19 seconds. All experiments are repeated 3 times for justifications. Comparing the RMSE of ACIR2017 and ACIR2020 using paired T-test shows no significant difference (p-value = 0.17). The total RMSE average of ACA method was 0.61 mm with a SD of 0.22 mm. The total time average required for analysing an image was 5.21 seconds with SD of 0.93 seconds. The statistical tests show that there is no difference between the results from automatic A-value method and the manual A-value method (p-value = 0.42). There is no difference also between length’s measurements of the left and the right ear sides (p-value > 0.16). Comparing the results from German and Egypt dataset shows there is no difference when using manual or automatic A-value methods (p-value > 0.20). However, there is a significant difference when using ACA2000 method between the German and the Egyptian results (p-value < 0.001). The average time to obtain the segmentation and all measurements was 5.21 second per image. The cochlea scala tympani volume size ranged from 38.98 mm3 to 57.67 mm3 . The combined scala media and scala vestibuli volume size ranged from 34.98 mm 3 to 49.3 mm 3 . The overall volume size of the cochlea should range from 73.96 mm 3 to 106.97 mm 3 . The lateral wall length of scala tympani ranged from 42.93 mm to 47.19 mm. The organ-of-Corti length of scala tympani ranged from 31.11 mm to 34.08 mm. Using the A-value method, the lateral length of scala tympani ranged from 36.69 mm to 45.91 mm. The organ-of-Corti length of scala tympani ranged from 29.12 mm to 39.05 mm. The length from ACA2020 method can be visualised and has a well-defined endpoints. The ACA2020 method works on different modalities and different images despite the noise level or the resolution. In the other hand, the A-value method works neither on MRI nor noisy images. Hence, ACA2020 method may provide more reliable and accurate measurement than the A-value method. The source-code and the datasets are made publicly available to help reproduction and validation of my result.