TAPAS: Towards Automated Processing and Analysis of multi-dimensional bioimage data

Modern microscopy is based on reproducible quantitative analysis, image data should be batch-processed by a standardized system that can be shared and easily reused by others. Furthermore such system should require none or minimal programming from the users. We developed TAPAS (Towards an Automated Processing and Analysis System). The goal is to design an easy system for describing and exchanging processing workflows. The protocols are simple text files comprising a linear list of commands used to process and analyse the images. An extensive set of 60 modules is already available, mostly based on the tools proposed in the 3D ImageJ Suite. We propose a wizard, called TAPAS menu, to help the user design her protocol by listing the available modules and the parameters associated. Most modules will have default parameters values for most common tasks. Once the user has designed her protocol, she can apply the protocol to a set of images, that can be either stored locally or on a OMERO database. An extensive documentation including the list of modules, various tutorials and link to the source code is available at https://imagej.net/TAPAS.

A web tool to linearize knowledge search

In Social Network analysis (SNA), we have a structure called Graphs, which has nodes and lines connecting those nodes. These lines are called edges. There is a metric in Graphs called distance. In an ideal Graph in SNA, each node should be connected to all of the other nodes, that is distance should be one. In this paper we are suggesting a Graph of scientific terminologies. There is a content corresponding to each scientific terminology and that content has tags (keywords). So the distance of the terminology to the tags of its content is one. Now those tags have their own content. So we have a Graph of terminologies. What we suggest is that as we build up the content in the website, we try to reduce the distance between the tags. This process in Graph terminology is called completing the Graph.So we are suggesting a Content Management System, where we want to build up quality scientific content. Apart from reducing the distance, we propose a method of making a linear list of tags, which linearizes the task of literature search. We discuss in the paper the advantages of the linearizing process.

Pengertian Linked Object

Dalam suatu linear list kita dapat melakukan operasi penyisipan atau penghapusan atas elemen-elemennya pada sembarang posisi.Misalkan ada 1500 item yang merupakan elemen dari suatu linear list.Jika elemen ke-56 akan kita keluarkan, maka elemen ke-1 s/d elemen ke-55 tidak akan berubah posisinya pada linear list tersebut. Tetapi elemen ke-57 akan menjadi elemen ke-56, elemen ke-58 akan menjadi elemen ke-57 dst. Selanjutnya, jika kita sisipkan satu elemen pada posisi setelah elemen ke-41, maka elemen ke-42 s/d elemen ke-1500 akan berubah posisinya.Untuk menyatakan keadaan diatas diperlukan suatu konsep yang berbeda dengan konsep sekuensial sebelumnya.Linked list merupakan suatu cara non-sekuensial yang digunakan untuk merepresentasikan suatu data.Kata Kunci : Linked list merupakan suatu cara non-sekuensial yang digunakan untuk merepresentasikan suatu data

DESCRIPTION AND IDENTIFICATION OF TEMPORAL REGULARITIES FOR FUZZY TIME SERIES WITH APPLICATION OF HYBRID OLS-PATTERNS

ObjectivesThe aim of the research is to develop the principle of storing data templates to take their temporal natureinto account, making it possible to reduce decision-making times.In order to describe and identify temporal patterns in fuzzy time series behaviour in real time, the task was set to develop a hybrid data structure that allows for a consideration of sequences of fuzzy values formed from clear observable data as well as a determination of the length of these sequences and possible uneven time intervals between the observations.MethodsThe article discussesan approach to formalising the description of temporal cause-effect relationships between events occurring at the object location as well as that of its environment, based on a set of singly-connected lists of triplets. Each triplet contains a fuzzy linguistic variable, the duration of its observation and the permitted interval of observation of insignificant data.ResultsAn algorithm for detecting knowledge base patterns in real time was developed, taking into account the possibility of a time shift in observing long sequences of identical values of the observed value. The possibility of partial data overlapping corresponding to triplets of different patterns is taken into account. The proposed hybrid pattern makes it possible to accelerate the detection of temporal regularities in the data.ConclusionScientific results are presented by the developed structure for storing information on temporal regularities in data, based on a singly linked linear list, as well as an algorithm for finding regularities in observational data using a set of OLS-patterns. The advantage of this structure and algorithm in comparison with the known ways of storing and analysing temporal data is a reduction in the amount of memory necessary for storing templates in the knowledge base, as well as the possibility of applying OLS patterns for decisionmaking purposes.

Linear list r-hued coloring of sparse graphs

An [Formula: see text]-hued coloring is a proper coloring such that the number of colors used by the neighbors of [Formula: see text] is at least [Formula: see text]. A linear [Formula: see text]-hued coloring is an [Formula: see text]-hued coloring such that each pair of color classes induces a union of disjoint paths. We study the linear list [Formula: see text]-hued chromatic number, denoted by [Formula: see text], of sparse graphs. It is clear that any graph [Formula: see text] with maximum degree [Formula: see text] satisfies [Formula: see text]. Let [Formula: see text] be the maximum average degree of a graph [Formula: see text]. In this paper, we obtain the following results: (1) If [Formula: see text], then [Formula: see text] (2) If [Formula: see text], then [Formula: see text]. (3) If [Formula: see text], then [Formula: see text].

Decidable linear list constraints

We present new results on a constraint satisfaction problem arising from the inference of resource types in automatic amortized analysis for object-oriented programs by Rodriguez and Hofmann.These constraints are essentially linear inequalities between infinite lists of nonnegative rational numbers which are added and compared pointwise. We study the question of satisfiability of a system of such constraints in two variants with significantly different complexity. We show that in its general form (which is the original formulation presented by Hofmann and Rodriguez at LPAR 2012) this satisfiability problem is hard for the famous Skolem-Mahler-Lech problem whose decidability status is still open but which is at least NP-hard. We then identify a subcase of the problem that still covers all instances arising from type inference in the aforementioned amortized analysis and show decidability of satisfiability in polynomial time by a reduction to linear programming. We further give a classification of the growth rates of satisfiable systems in this format and are now able to draw conclusions about resource bounds for programs that involve lists and also arbitrary data structures if we make the additional restriction that their resource annotations are generated by an infinite list (rather than an infinite tree as in the most general case). Decidability of the tree case which was also part of the original formulation by Hofmann and Rodriguez still remains an open problem.