Multi_Scale_Tools: A Python Library to Exploit Multi-Scale Whole Slide Images

For instance, Khorasani et al [185] proposed an adaptive filtering method using weighted common average reference filter, and decoded kinematic force information based on both LFP and MUA with a partial least square model. The decoding accuracy using the LFP and MUA outperformed models that relied solely on either LFP or MUA. The authors suggested that LFP and MUA may have information that is different or supplementary in terms of the covariates they investigated.

multi-scale analysis tools

Training the regressor with patches from several organs may allow to close this gap, guaranteeing extremely high performance for different types of tissue. Rather than improve performance and compute times with a small training sample, many provide either improved performance or reduction in necessary sample size. These methods also require a high degree of statistical expertise that many practitioners may not have.

4 Multi-Scale CNN for Segmentation

Therefore, the scripts to train them need a set of patches and the corresponding magnification level as input, which are provided into csv files, including the patch path and the corresponding magnification levels. Two scripts are developed to generate the input files, assuming that the patches are previously generated with the pre-processing components, described in the previous section. The first script is made to split the WSIs into partitions (, which generates three files (the input data for training, validation and testing partitions) starting from three files (previously prepared by the user) including the names of the WSIs.

  • This technique was exploited for EEG-based neurofeedback training in soldiers facing stressful military combat training [43].
  • For this reason, the CNNs show high performance with patches from magnification 5/10x, while including patches from 20x decreases the performance.
  • These methods also require a high degree of statistical expertise that many practitioners may not have.
  • It outperforms the best single-scale CNN (trained with patches acquired at 5x) in terms of balanced accuracy, while the κ-score of the two architectures is comparable.
  • The methods identified to pair images from several magnification levels can pave the way to multi-modal combination of images too.
  • We then present our case for integrating activity across multiple scales to benefit from the combined strengths of each approach and elucidate a more holistic understanding of neural processes as well as more robust strategies for decoding information from the brain.

The first multi-scale CNN architecture, in which features are combined from different scale branches, optimizing only one loss function (A) and optimizing n + 1 loss function (B). With this approach, engineers are able to perform component and subcomponent designs with production-quality run times, and can even perform optimization studies. These methods are certainly more accurate than their single-scale, isotropic predecessors, but fall short when trying to analyze novel parts/materials for which there is no historical correlations or empirical guide-posts.

1 Image Multiscale Decomposition

Subsequent TEM analysis provides atomic-scale materials characterization for complete insight into a sample’s elemental and structural composition. Urbach and Wilkinson (2002) and Urbach et al., (2007) extended the theory of granulometries to define shape granulometries. To exclude sensitivity to size, the operators used can generally not be increasing, as was shown in Urbach & Wilkinson (2002) and Urbach et al. (2007). We start with MSA, i.e. we establish algorithms to decompose a spline into an orthogonal sum of type (4.1.2) and to reconstruct it. Scale invariance, fractal statistics, the fractal dimension and measures of selfsimilarity also provide insight into the relationship between scales within a system. For example, these techniques may reveal limits to the utility of averages, the dependence of a measure on the scale of measurement, and the mutual information between scales of a system.

multi-scale analysis tools

Indeed, the edges are quickly damaged by the usual ASFs (Figure 19b–fig20d), while they are preserved with the connected ASFs. Moreover, the filters by reconstruction remove fine details (as revealed in the scene on the camera), for the eye of the human face and for the buildings (Figure 19e–fig20g), although they are connected. On the contrary, the decomposition of the original image with ANMM-based filters does not decimate relevant structures from fine-to-coarse scales (Figure 19h–j). One approach to analysing multiscale systems with emergent properties is the complexity profile, which analyses the amount of information required to describe a system at every scale [Bar-Yam, 2004]. The complexity profile of an organisation can reveal how well it matches the complexity of its environment, and identify whether either increasing fine scale variety or enhancing large scale coordination is likely to improve the organisation’s fitness. We define semi-analytical methods as direct micro/macro procedures for which the local constitutive equations and criteria are evaluated at the local scale and explicit relations are used to establish the link between the macroscopic behavior with microstructural responses.

Signal and Image Representation in Combined Spaces

advanced materials accurately is extremely complex because of the high number
of variables at play. The materials in question are heterogeneous in nature,
meaning they have more than one pure constituent, e.g. carbon fiber + polymer
resin or sedimentary rock + gaseous pores. In the language used below, the quasicontinuum method can be thought of as
an example of domain decomposition methods.

Work to date has conventionally focused on neural activity acquired using a single modality and, thus, at a single scale. Decoding and modeling neural dynamics using measurements from one modality limits investigations to dynamics within the same level. However, complex spatiotemporal activity supports behavior and cognition, and cross-scale dynamics can reveal a deeper and more comprehensive understanding of system-level neural mechanisms [19, 20]. Uncovering multi-scale dynamics is essential for illuminating the mechanistic understanding of brain function and to harness scientific insight for neuroscientifically grounded clinical treatment. A paradigm shift, enabled by state-of-the-art neurotechnologies, is currently underway to analyze neural activity across multiple scales. Computational pathology is the computational analysis of digital images obtained through scanning slides of cells and tissues (van der Laak et al., 2021).


These platforms have been widely investigated as a method to assist impaired individuals’ ability to interact with the world around them. However, certain challenges exist that limit the usability of BMIs, such as the requirement to optimize control features and identify successful mental strategies to properly control a device [242]. Additionally, a phenomenon known as 'BMI illiteracy’ exists, in which around 15%–30% of individuals are unable to learn to control a BMI [243]. Multimodal approaches have been suggested to address these challenges by providing the BMI with more detailed information from the temporal dynamics of electrical activity and the hemodynamic fluctuations in the cortex [242]. This can improve a BMI’s ability to decode the user’s intention which leads to better usability and control [244, 245]. One line of research in this domain showed that striatal BOLD responses correlate with relative dopamine D2/D3 receptor occupancy in the striatum of non-human primates [218].

The vertical axis shows the area, the horizontal the first-moment invariant of Hu of image features in each bin; brightness indicates the power in each bin. (b) One selected bin in each spectrum and the corresponding image details are highlighted by a hatch pattern. Thus, a shape granulometry is an ordered set of operators that are anti-extensive, scale-invariant, and idempotent. To exclude sensitivity to size, we add property (54), which is just scale invariance for all ψr. The absorption property (55) is easily achieved by using any scale-invariant attribute combined with a criterion of the form in Eq.

Wavelet based multi-scale analysis of financial time series has attracted much attention, lately, from both the academia and practitioners from all around the world. The unceasing metamorphosis of the discipline of finance from its humble beginning as applied economics to the more sophisticated depiction as applied physics and applied psychology has revolutionized the way we perceive the market and its complexities. One such complexity is the presence of heterogeneous horizon agents in the market. In this context, we have performed a generous review of different aspects of horizon heterogeneity that has been successfully elucidated through the synergy between wavelet theory and finance.

The renormalization group method has found applications in a variety
of problems ranging from quantum field theory, to statistical physics,
dynamical systems, polymer physics, etc. Multiscale ideas have also been used extensively in contexts where no
multi-physics models are involved. When studying chemical reactions involving large molecules, it often
happens that the active areas of the molecules involved in the
reaction are rather small. The rest of the molecules just serves to
provide the environment for the reaction.