SpineTool is an open-source software for analysis of morphology of dendritic spines.

Dendritic spines form most excitatory synaptic inputs in neurons and these spines are altered in many neurodevelopmental and neurodegenerative disorders. Reliable methods to assess and quantify dendritic spines morphology are needed, but most existing methods are subjective and labor intensive. To solve this problem, we developed an open-source software that allows segmentation of dendritic spines from 3D images, extraction of their key morphological features, and their classification and clustering. Instead of commonly used spine descriptors based on numerical metrics we used chord length distribution histogram (CLDH) approach. CLDH method depends on distribution of lengths of chords randomly generated within dendritic spines volume. To achieve less biased analysis, we developed a classification procedure that uses machine-learning algorithm based on experts' consensus and machine-guided clustering tool. These approaches to unbiased and automated measurements, classification and clustering of synaptic spines that we developed should provide a useful resource for a variety of neuroscience and neurodegenerative research applications.

Three-Dimensional Reconstruction of Pelvicalyceal System of the Kidney Based on Native CT Images Are 1-Step Away from the Use of Contrast Agent.

OBJECTIVE: To describe special algorithm for the semi-autonomous 3-dimensional reconstruction of the pelvicalyceal system based on native computed tomography images of patients with upper urinary tract obstruction. MATERIALS AND METHODS: Fifty patients with renal colic fitting to inclusion criteria were enrolled. All patients underwent computed tomography urography to perform 3-dimensional reconstruction of the pelvicalyceal system on the affected size based on excretory phase representing "gold standard" and on native phase, which was performed via Medical Imaging Interaction Toolkit program updated with the described algorithm. Five urologists estimated their similarities and the potential use of non-contrast models for interventional planning. Contralateral non-distended pelvicalyceal system was reconstructed to evaluate the viability of the proposed technology in such cases. Surface areas of contrast and non-contrast models were compared. Distended pelvicalyceal system of 1 patient was used to reconstruct virtual endoscopic view. Obtained 3-dimensional noncontrast pelvicalyceal system models were analyzed by an engineer for suitability for 3-dimensional printing. RESULTS: The average surface area of contrast and non-contrast models was 3513 and 3371 mm2 , respectively (P=.0818). Non-contrast 3-dimensional reconstruction was possible with all distended pelvicalyceal systems and with 9 non-distended cases. Properties of non-contrast models were estimated as 4.3 out of 5. Obtained models were suitable for their intraluminal reconstruction and potential 3-dimensional printing. CONCLUSION: Described semi-autonomous approach allows for 3-dimensional reconstruction of dilated pelvicalyceal system based on non-contrast computed tomography images.