Biological shape analysis (under construction) – bioshape-analysis

Categories

All (33)

AFM (2)

Benamou-Brenier's Formulation (2)

Cell Migration (2)

Cell Morphology (2)

Differential Geometry (2)

Graph theory (1)

Kantorovich's Formulation (1)

MATH 612 (1)

MDS (1)

Math 612D (1)

Monge's Problem (1)

Vascular Networks (1)

agriculture (1)

automatic differentiation (1)

bioinformatics (10)

biology (12)

biomedical engineering (1)

cell morphology (1)

cryo-EM (5)

cryo-ET (1)

cryo-em (2)

example (1)

landscape-analysis (1)

mathematics (1)

neuroscience (1)

optimal transport (2)

pytorch (1)

ribosome (3)

shape morphing (2)

theory (4)

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MATH 612

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An analysis and segmentation of contours in AFM imaging data

biology

AFM

The segmentation of pieces in AFM images gives us a chance to gather information about their shape. This can very well be a determining characteristic for certain biological…

Optimal Mass Transport for Shape Progression Study

PyTorch Implementation of Benamou-Brenier Formulation

optimal transport

shape morphing

Benamou-Brenier’s Formulation

pytorch

automatic differentiation

In this blog post, let us continue from the previous blog post on defining the convex formulation of optimal mass transport (OMT). Specifically, let us look upon the need…

Shape analysis of C. elegans E cell

biology

Some more background information in the blog post link.

Viktorija Juciute

Farm Shape Analysis: Linking Geometry with Crop Yield and Diversity

landscape-analysis

agriculture

In modern agriculture, the geometric features of farmland play a crucial role in farm management and planning. Understanding these characteristics enables farmers to make…

Landmarking the ribosome exit tunnel

ribosome

cryo-em

bioinformatics

I present a complete Python protocol for assigning landmarks to the ribosome exit tunnel surface based on conservation and distance. The motivation and background for this…

Extensions to RECOVAR for heterogeneity analysis of SARS-CoV2 spike protein from cryo-EM data

cryo-EM

In the previous post Heterogeneity analysis of cryo-EM data of proteins dynamic in comformation and composition using linear subspace methods, we reviewed the pipeline of…

Identifying R-loops in AFM imaging data

biology

AFM

R-loops are three-stranded nucleic acid structures containing a DNA:RNA hybrid and an associated single DNA strand. They are normally created when DNA and RNA interact…

Vascular Networks

Graph theory

Vascular Networks

I have introduced some basic concepts of micro-circulation and the vascular networks and how they get created (angiogenesis) in health and disease. Then I discuss some…

Ali Fele Paranj

Shape Analysis of Contractile Cells

biology

cell morphology

Capsular contracture (CC) is an ailing complication that arises commonly amonst breast cancer patients after reconstructive breast implant surgery. CC patients suffer from…

Exploring cell shape dynamics dependency on the cell migration

Cell Morphology

Cell Migration

Differential Geometry

Cell morphology is an emerging field of biological research that examines the shape, size, and internal structure of cells to describe their state and the processes…

Pavel Bukleomishev

Exploring cell shape dynamics dependency on the cell migration

Cell Morphology

Cell Migration

Differential Geometry

Cell morphology is an emerging field of biological research that examines the shape, size, and internal structure of cells to describe their state and the processes…

Pavel Buklemishev

Embryonic cell size asymmetry analysis

biology

Cells propagate via cell division. In multicellular organisms, certain cells divide asymmetrically, which results in generating cell diversity (Jan and Jan 1998). There are…

Viktorija Juciute

Trajectory Inference for cryo-EM data using Principal Curves

Math 612D

Suppose you run an experiment that involves collecting data points \(\{\omega_1, \ldots, \omega_M\} \subseteq \Omega \subseteq \mathbb R^d\). As an example, suppose that \(\O…

Forest Kobayashi

Defining landmarks for the ribosome exit tunnel

ribosome

cryo-em

bioinformatics

The ribosome is present in all domains of life, though exhibits varying conservation across phylogeny. It has been found that, as translation proceeds, the nascent…

Optimal Mass Transport and its Convex Formulation

optimal transport

shape morphing

Monge’s Problem

Kantorovich’s Formulation

Benamou-Brenier’s Formulation

In the context of biomedics, understanding disease progression is critical in developing effective diagnostic and therapeutic strategies. Medical imaging provides us with…

Heterogeneity analysis of cryo-EM data of proteins dynamic in comformation and composition using linear subspace methods

cryo-EM

Cryogenic electron microscopy (cryo-EM), a cryomicroscopy technique applied on samples embedding in ice, along with recent development of powerful hardwares and softwares…

Understanding Animal Navigation using Neural Manifolds With CEBRA

biology

bioinformatics

mathematics

biomedical engineering

neuroscience

Seeing, hearing, touching – every moment, our brain receives numerous sensory inputs. How does it organize this wealth of data and extract relevant information? We know that…

Extracting cell geometry from Atomic Force Microscopy

Part 2: Temporal amd morphological analysis

biology

bioinformatics

Clément Soubrier, Khanh Dao Duc

Horizontal Diffusion Map

theory

This post is based on the following references:

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

biology

bioinformatics

Multidimensional scaling (MDS) is known to be sensitive to such orthogonal outliers, we present here a robust MDS method, called DeCOr-MDS, short for Detection and Correction…

Centroidal Voronoi Tessellation

Relations with Semidiscrete Wasserstein distance

theory

In this post we briefly explained Centroidal Voronoi Tessellation (CVT) as a point sampling method and how it rises from the Optimal Transport (OT) theory. Here we will…

Aryan Tajmir Riahi

Simulation of tomograms of membrane-embedded spike proteins

cryo-ET

Cryogenic electron tomography (cryo-ET) is an imaging technique to reconstruct high-resolution 3d structure, usually of biological macromolecules. Samples (usually small…

Shape Analysis of Cancer Cells

biology

bioinformatics

This notebook is adapted from this notebook (Lead author: Nina Miolane).

Riemannian elastic metric for curves

biology

bioinformatics

This page introduces basic concepts of elastic metric, square root velocity metric, geodesic distance and Fréchet mean associated with it.

Point cloud representation of 3D volumes

Application to cryoEM density maps

biology

bioinformatics

In the context of cryo-EM, many computationally exhaustive methods rely on simpler representations of cryo-EM density maps to overcome their scalability challenges. There…

Aryan Tajmir Riahi, Khanh Dao Duc

Multi Dimensional Scaling of ribosome exit tunnel shapes

Analyze and compare the geometry of the ribosome exit tunnel

cryo-EM

ribosome

MDS

The ribosome exit tunnel is a sub-compartment of the ribosome whose geometry varies significantly across species, potentially affecting the translational dynamics and…

Shiqi Yu, Artem Kushner, Khanh Dao Duc

Alpha Shapes in 2D and 3D

theory

Alpha shapes are a generalization of the convex hull used in computational geometry. They are particularly useful for understanding the shape of a point cloud in both 2D and…

Quasiconformal mapping for shape representation

theory

Clément Soubrier

3D tessellation of biomolecular cavities

Protocol for analyzing the ribosome exit tunnel

cryo-EM

We present a protocol to extract the surface of a biomolecular cavity for shape analysis and molecular simulations.

Artem Kushner, Khanh Dao Duc

Alignment of 3D volumes with Optimal Transport

Application to cryoEM density maps

example

cryo-EM

Aryan Tajmir Riahi, Khanh Dao Duc

Extracting cell geometry from Atomic Force Microscopy

Part 1: Static analysis

biology

bioinformatics

We present here the protocole to process biological images such as bacteria atomic force miroscopy data. We want to study the bacteria cell shape and extract the main…

Clément Soubrier, Khanh Dao Duc

Analysis of Eye Tracking Data

bioinformatics

Eye tracking (ET) is a process by which a device measures the gaze of a participant – with a number of variables that can be captured, such as duration of fixation…