Software

Description: Automated 3D Axonal Morphometry of WhiteMatter pipeline.

Author(s): Abdollahzadeh A, Belevich I, Jokitalo E, Tohka J & Sierra A

Description: ADL achieves state-of-the-art Gaussian denoising performance in grayscale/color image denoising in Medical imaging, computer vision images. 

Author(s): Ghahremani M, Khateri M, Sierra A & Tohka J

Description: Two-dimensional X-ray tomography is one of the basic examples in the book Mueller & Siltanen: Linear and nonlinear inverse problems with practical applications (SIAM 2012). This learning resource offers presentation slides and Matlab codes that Professor Samuli Siltanen used at the winter school Advanced methods for mathematical image analysis in Bologna, Italy, January 2023.    

Author(s): Siltanen S

Description: A tool for automated counting of cells in Nissl stained sections.

Author(s): Ali Abdollahzadeh

Description: CTlab is virtually implemented medical imaging device.

Author(s): Ylisiurua S, Brix M, Liimatainen T, Hanni M & Nieminen M

Description: The ddeq Python library for point source quantification from remote sensing images (Version 1.0).

Author(s): Kuhlmann G et al.

Description: Automated Segmentation of White Matter in 3D large Electron Microscopy data pipeline.

Author(s): Abdollahzadeh A, Belevich I, Jokitalo E, Sierra A & Tohka J 

Description: One-dimensional deconvolution is one of the basic examples in the book Mueller & Siltanen: Linear and nonlinear inverse problems with practical applications (SIAM 2012). It is very educational to study how Tikhonov regularization, Total Variation regularization and wavelet sparsity sharpen blurred signals, each in their own way.     

Author(s): Siltanen S & Murthy R 

Description: The DendriteSAM model, designed for dendritic segmentation in electron microscopy images.

Author(s): Zhuo Z

Description: Scripts to perform edge-path bundling (Wallinger et al. 2022) for flow data. It’s primary use case is to support visualization of complex mobility data, and has been used to bundle human mobility flows across NUTS regions in Europe.

Author(s): Väisänen T, Inkeröinen O, Malekzadeh M & Järv O

Description: Pilot for Africa: Space-based service for greenhouse gas and air pollution hotspot emission monitoring.

Author(s): Hakkarainen J, Ialongo I, Virta H & Niemitalo O

Description: gACSON software is to visualize, segment, and analyze the morphology of neurons in three-dimensional electron microscopy images.

Author(s): Behanova A, Abdollahzadeh A, Belevich I, Jokitalo E, Sierra A & Tohka J 

Description: GDE-FEM 2.0 code package simulates temporal evolution of aerosol size distributions by approximating condensation/evaporation, coagulation, formation, and removal processes. These phenomena are described with General Dynamic Equation of Aerosols (GDE), which is discretized by utilizing finite element method (FEM) and its extension, Petrov-Galerkin FEM.

The code package is applicable for single and multi-component cases. Usage of code package requires some knowledge of MATLAB syntax as inputs and changes must be made directly into the code in current version. 

Author(s): Salminen T

Description: HAPI2LIBIS enables easy creation of spectral molecular absorption files for the radiative transfer simulator software LibRadtran.

Author(s): Kukkurainen A & Mikkonen A

Description: High-dimensional Kalman filter toolbox (HELMET) is an open-source software for high-dimensional linear dynamic problems. HELMET includes various KF algorithms that can be used to estimate any linear dynamic problems. The core idea of HELMET is the use of GPUs for the fast computation of Kalman filter.

Author(s): Wettenhovi V-V 

Description: Helsinki Tomography Toolbox (HelTomo) is a MATLAB toolbox that has been primarily created for working with X-ray Computed Tomography (CT) data measured in the Industrial Mathematics Computed Tomography Laboratory at the University of Helsinki. Its purpose is facilitate a fast and easy workflow from raw projection data to reconstructions, allowing researchers to test their CT algorithms on real, measured X-ray data. 

Author(s): Meaney A

Description: LeafGen is an open source MATLAB package containing methods for generating virtual foliage on 3D tree models based on parametric leaf distributions.

Author(s): Mönkkönen P

Description: LinTim is a scientifc software library for optimization in public transport.

Author(s): Schiewe P, Schöbel A, Herrala O, Rihlmann M, Roth S, Albert S, Biedinger C, Dahlheimer T, Dittrich L, Hoffmann K, Jäger S, Pattanaik P, Schiewe A, Stinzendörfer M & Urban R

Description: MCMCstat is a popular Matlab toolbox for Bayesian parameter estimation in non-linear models using Markov chain Monte Carlo (MCMC) simulation. It implements the traditional Metropolis-Hastings algorithm along with various adaptive algorithms. 

Author(s): Laine M

Description: Multi-view feature selection based on multi-chromosome architectures.

Author(s): Imani V

Description: OMEGA, open-source multi-dimensional tomographic reconstruction software, is an image reconstruction toolkit for tomographic imaging, optimized for positron emission tomography (PET), single photon emission computed tomography (SPECT) and computed tomography (CT). However, any ray-tracing based tomographic imaging is supported.

Author(s): Wettenhovi V-V, Summala S, Kangasniemi J, Manninen A, George A & Kortelainen M 

Description: OOEIT (Object Oriented Electrical Impedance Tomography) is an open-source Matlab code package for computing electrical impedance tomography (EIT) simulations and reconstructions. It is designed for ease of use for those with no deep understanding of EIT, while also featuring a modular structure that allows for straightforward customization for those interested in developing their own algorithms. 

Author(s): Kuusela P

Description: Example pipelines to run different T1w-MRI processing tools in an HPC-like environment.

Author(s): Tohka J, Salo R, Mäki-Maunus T & Farki A

Description: Monochromatic scalar 3D radiative transfer model.

Author(s): Mikkonen A

Description: ValoMC is an open source Monte Carlo code that can simulate light propagation in a scattering medium.

Author(s): Leino A, Pulkkinen A, Lunttila T & Tarvainen T