This article is a comprehensive review of software programs used in biomedical research, based on randomly selected, formal publications with citations of specific software programs, within a cohort of over 10,000 articles that Labome has manually surveyed since 2006. The dataset comprises of methodologies like data searching, acquisition, analysis, prediction and computational modeling, and simulation like COMSOL Multiphysics [1].

The programs are grouped based on their applications. Table 1 lists the groups and the numbers of articles. Several groups involved in image analysis form the largest area of applications. "Cell and tissue imaging system and analysis software" refers to those sets for analyzing cell or tissue images, generally under microscopes, such as phase-contrast and immunohistochemical staining images. "Blot image analysis software" refers to the software applications for gel images or results from Southern, Northern, or Western blotting. Each group is discussed in detail later. One important point about the number of articles cited by each software is that only software explicitly discussed in the articles is tabulated. There are many cases where the use of specific software is implied, especially when a specific instrument such as a PCR machine or a DNA sequencer is employed. In such cases, no software citation is considered. The software programs used for statistical analysis are considered in a separate article.

Cellular imaging is one of the most applied techniques to obtain information and provide visual evidence of their presence in living cells. Advanced microscopes can see details down to the diffraction limits or some hundreds of nanometers or even go smaller, with the super-resolution techniques. Image analysis such as densitometric quantification, determination of cell length, cell size and number, the relative fluorescence intensity of different fluorophores is necessary and the data is used for comparison between samples. Table 2 lists the image analysis software programs cited most often among the articles Labome has surveyed.

In order to take an image, the microscope with its components has to be controlled through a software. This software is either provided by the main microscope constructors or can be an open source solution. Table 3 lists the main microscope control software with their characteristics. All the software offer image analysis options, that can be basic (2D, time lapse visualisation) or more complex (3D, deconvolution, automatization).

A proprietary software of Carl Zeiss Microscopy comes in both Biology and Materials version. One of the first Zeis software was the .net framework (Windows) based AxioVision for Biology that performs 5 major functions: image acquisition; image processing; image analysis; image archiving; and software configuration. Each function is in turn helped by different modules performing complementing tasks to acquire more information from the subject of study. For example, of the 14 modules in Image Acquisition, the dual camera module by name can allow using two of the modules simultaneously, tissue microarrays offers large scale analysis, panorama provides an overview idea about the images captured apart from the high definition, high speed and fast acquisition modules that can help acquire large quantity of information at shorter intervals at high resolution. AxioVision offers image processing methods like deconvolution, imaging plus to enhance the quality of images and provide the 4th dimension of time to 3D images using Inside4D module. The ASSAYbuilder module allows to perform high content screening and analysis relating to cell-based tests like cytotoxicity, apoptosis, cell differentiation, molecule localization and reporter expression. As diverse as 50 different parameters of 3D measurements can be obtained and allow interactive measurement. The software can do auto-measurements and be programmed for the same with programming routines. It can also perform cell tracking and provide related measurements. The Physiology module is incorporated with FRET capabilities and control fluorescence signals over all microscope components. It can capture about 140 frames per second with AxioVision HS. The Visual Basic for Applications (VBA) for AxioVision offers free hand within its own limits to design functionality based application development. Finally, the images, captured and analyzed, can be recorded as per FDA standards based on Regulation 21 CFR Part 11. The AxioVision GxP auto starts once the OS opens and surveys hard-disks for files and folders thereby can track and document each performed transaction in separate XML files.

Carl Zeiss AxioVision software, for instance, was used to investigate the role of hybrid Th1/2 cells in natural immune responses against parasites [9], the role of CDON in regulating tumor cell survival [10], to analyze the morphologies of cutaneous sensory neuron arbors in hairy skin of the mouse [11] and the cellular origin of adult functional blood vessels [12], to study amino acid homeostasis [13], fetomaternal immune tolerance [14] and the inhibition of protein translation by miR430 in zebrafish [15]. AxioVision multidimensional acquisition mode was used to perform time-lapse image acquisition to study calcium signaling by PKG and its physiology module was used to analyze the fluorescence of individual ookinetes [16].

In addition to AxioVision, Zeiss LSM Image Browser was also often cited. It was used to perform real-time redox imaging to study the regulation of SCN neurons through circadian changes of redox state [17], among other applications [13, 18-23].

The last years AxioVision software is gradually replaced by the ZEN Blue and ZEN Black (table 3). ZEN Blue was mainly used to control the wide-field microscopes of Zeiss. Nowadays, it is replacing the ZEN Black software, which controls the confocal microscopes. It offers 2D analysis and a 3D visualization option. There is a deconvolution algorithm as an option. One important feature of ZEN is the Experimental Designer, that creates Blocks which can automatize the pipeline acquisition - analysis.

The Nikon software is the NIS Elements. It controls the Nikon microscopes. It offers 2D analysis, 3D visualization and a deconvolution module. A very interesting module of NIS is JOBS, an experiment builder, that offers automatization of tasks and is quite easy to use.

The Leica microscope control and analysis software is the LAS. It controls all Leica microscopes. It offers the standard 2D analysis, 3D visualization, deconvolution and some basic analysis tasks, like plotting intensity profiles, measure distances, etc.

The Olympus software is the CellSens. It offers the basic 2D analysis, 3D visualization, deconvolution. Thanks to the Graphic Experiment Management and the Well Navigator it offers some basic automatization tasks. Its proper characteristic is that it is a very visual software, quite easy to understand and to use.

Andor commercializes some microscopes the last years (mainly spinning disks). The control and analysis software was at the beginning the iQ3. It is a basic software, and one can easily establish its proper acquisition protocol. For the most recent Andor microscopes like the Dragonfly series, Andor proposes the Fusion software, which is easier to use and has some interesting analysis modules, like the 3D visualization coupled to Imaris software and the deconvolution module.

Softworx is a visualization and analysis software from Applied Precision (GE Healthcare). It combines image viewing, processing and analysis tools with data management software in an easy-to-use format. The software comes with a real-time viewer with channel select, z and time control. It can perform 4D measurement and animation, batch mode operation and send, access through FTP/SFTP. It performs baseline removal, measurement with free points, slice points and surface points, does image correction and restoration by deconvolution. While its advantages are felt in the co-localization analysis package where it is easy to isolate, visualize, and quantify regional overlap in 3D and 4D images with results presented in two ways, a new 3D or 4D channel as well as a statistical report. For instance, Applied Precision softWoRx v 5.0 was used to perform the reconstruction and alignment of 3D-SIM images to study the molecular architecture of SpoIIIE pump and the mechanism of its recruitment and assembly [24]. The limitations are many as it is not an all-encompassing tool to perform a wide range of studies but restricted.

MetaMorph software by Molecular Devices was initially included by many microscope hardware providers before the providers started to offer their own version of microscope control and image analysis software. MetaMorph can read the libraires (DLL) of the microscope components, so for the microscope to be controlled, one needs to have a MetaMorph version that recognizes its components. With the years, MetaMorph should be able to provide updates for the new microscope components that come out (cameras, stages, etc) in order for the software to continue controlling the new microscopes.

MetaMorph is a basic software, easy to use, that at the same time offers many analysis options.

The multi-dimensional acquisition module enables both simple and guided user interface to perform complex acquisition sequences. The image or video acquired is simultaneously transferred to memory so as to ease the hardware acceleration for image capture. The images are linked to related graphs and tables thus helping the user to correlate the images and the data. The Live Replay module supported by this feature of copying back to memory can help capture real-time events from FRET, FRAP, live imaging and time-lapse experiments The scan slide module aids in stitching a series of images from a large section of tissue sample providing a reproducible high-resolution image cutting the error from tilling experiments. For instances, Molecular Devices MetaMorph software was used to investigate the influence of cytokine expression on T helper cell differentiation [25], the roles of Vav2 and Vav3 in skin cancer [26], DNA looping induced by transcription factors in E. coli [27], the regulatory role of Erf2 in protein palmitoylation and meiotic entry in Schizosaccharomyces pombe [28], accurate timekeeping controlled by a cycling activator in Arabidopsis [29], the role for PICK1 and ICA69 in regulating the formation and maturation of insulin granules [30], the role of cell adhesion and cortex tension in cell sorting during gastrulation [31], the regulation of retrograde synaptic signal by NRX-1 and NLG-1 in C.elegans [32], the role of Ras/Epac2 pathway in maintaining basal dendrite complexity of cortical neurons [33] and the involvement of septin rice blast fungus infection [21]. The siblings of MetaMorph, Metavue and MetaXpress, have been used to perform confocal imaging to study the passive advective transport [34] and to capture wide-field images to study the role of XIAP in caspase inhibition after skeletal muscle differentiation [35].

Another software that controls microscopes is Labview (National Instruments). Labview is a system-design platform and development environment for a visual programming language. It offers a graphical programming approach that helps to visualize every aspect of the application, making it simple to integrate hardware from the vendors and design custom user interfaces. It is a software more dedicated to microscope developers, who wish to have a flexibility on the design of the components control. Like MetaMorph the components should be recognized by Labview with their DLL. It can offer custom user interfaces, for the control of the components, the visualization and the automatization of the imaging tasks.

Micromanager is a software package that can control microscopes. It is freeware and can be combined with the open source ImageJ software, to provide a complete solution for controlling microscopes and offering afterwards image analysis modules. Micromanager can read specific microscope hardware. If the hardware to be controlled is not at the supported micromanager list, one can address directly to micromanager community and perhaps a development can be made for the specific hardware support.

The data that comes out from the microscope acquisitions needs to be visualized and analyzed. When 3D imaging methods are implemented or even 4D (time lapse), then data becomes big in size and it is more difficult to first visualize and then analyse. The last years there is a bunch of software dedicated to 3D and 4D visualization of big data. Big datasets for microscopy are in the Terabyte range. With the progress of microscopy and the emerging imaging methods, like light sheet microscopy, the production of big data is inevitable and visualizing and treating big data is more than necessary. Table 4 shows the main 3D/4D visualization and analysis software for microscopy.

The software can be divided into 2 big families. On the one hand we find the commercial solutions and on the other hand solutions coming out from research laboratories which are often open-source.

Regarding the commercial solutions, the most used one is Imaris software from Bitplane. It is an interactive visualization and analysis software for 3D and time lapse microscopic images with advanced solutions for big datasets.

It uses a file format based on the standard HDF5 (Hierarchical Data Format 5) that allows using HDF5 libraries and tools for an easy visualization of the data set and then a more thorough analysis when more details are needed. It stores not only the original image data but also lower resolution versions of the original data. This allows the visualization software to load only low resolution data when those are sufficient.

In parallel, Imaris offers a number of analysis solution, like automated detection of cells and organelles, filaments tracer for neuron structures and not only, colocalization analysis, single particle tracking algorithms, deconvolution, tilescan stitching for big area imaging. At the same time it can create links to a custom analysis with other software like Matlab, Java, R or Python.

One of the main inconvenient of Imaris is that very powerful PC are needed as for for big data there is a big consumption of RAM and disk space. The list of published work from teams using imaris for 3D rendering and analysis is very long, as this is probably nowadays the most used software for these applications.

Another powerful commercialized software for 3D/4D visualization is Vision4D from Arivis (Table 4). It offers a high interactive rendering, even on standard PCs with a simple 3D graphics support. It is possible to establish workflows with Matlab and Python. Thanks to the efficient and easy rendering of 4D data, it was possible in 2019 to visualize images from combined expansion and lattice light sheet microscopy. They throw light on neural circuits across the whole drosophila brain and mouse primary somatosensory cortex [36].

An older software for 3D visualization is Volocity from Quorum Technologies. It offers a Free Viewer and it is easy to use. On the other hand, it does not offer many analysis modules.

A very recent and innovative software for 2D-5D analysis and visualization is the Aivia (DRVISION). Aivia delivers interesting solutions on critical tasks such as display of large images and analysis of complex biological phenomena. It is powered by a range of machine learning technology for both image segmentation, object classification and novelty detection. It is not yet coupled to many analysis modules.

The other big family of 3D/4D visualization and analysis software are the solutions that come from research laboratories and most often are open-source. There are three different plugins that are ready to use and implemented to the ImageJ/Fiji image analysis software (Java based). The first one and the most common one is the plugin BigSataViewer developed by the researcher T. Pietzsch (MPI-CBG Dresden) [37]. It handles quite well big data implemented the HDF5 format. It is a visualization solution solution with not many analysis options. The second plugin is the ClearVolume initiated by L. Royer [38]. It is a visualization plugin enabling the live 3D observation of specimens with a live data streaming mode. It has a dedicated interface to micromanager/OpenSpim control software in order to control live these light sheet instruments. The third plugin is the SciView from K. Harrington (University of Idaho) and U. Guenther (MPI-CBG). This plugin provides 3D visualization and virtual reality representation.

Another software dedicated to 3D/4D image visualization and analysis is the Vaa3D. It is maintained by both HHMI - Janelia Research Campus and the Allen Institute for Brain Science, and is used in a number of projects worldwide [39]. It is open source. It is fast and offers different plugins for further image analysis.

A promising software for interactive visualization of time lapsed volumetric data generated by light sheet microscopes is Spimagine, using a python package (M. Weigert, MPI-CBG). The package provides a generic 3D+t data viewer and makes use of GPU acceleration via OpenCL, offering a fast visualization solution.

Table 5 lists the major suppliers and their main software for molecular biology applications cited among the articles Labome has surveyed. Same as the cell and tissue image software, the majority of the suppliers for molecular biology software also provide the hardware systems such as sequencers and PCR instruments. Other molecular biology software programs, such as Blast2GO [40], are gaining popularity.

Applied Biosystems is one of the major providers for molecular biology instruments such as PCR or qPCR and gene sequencers. Applied Biosystems Primer Express and SDS software were used for PCR or qPCR to study the inhibition of oscillator gene expression [41] and the organization of gene expression [42], among others [43-55]. And its GeneMapper was cited in articles for gene scan [56-58].

Illumina BeadStudio, CASAVA, ELAND and Pipeline were used for SNP genotyping, and sequencing of ChIP, exome, transcriptome and RNA [41, 59-70].

Bio-Rad Opticon and LaserSharp programs were used for PCR to study the molecular mechanism of memory consolidation [71], among others [71-76].

SoftGenetics, unlike all the above providers, is a software company without any hardware products. Its Mutation Surveyor and GeneMarker programs were used to DNA sequencing analysis [77-79], genotyping [80], microsatellite analysis [81], and poly(A) tail length analysis [15].

Gene Codes Corporation, a bioinformatics company, provides Sequencher for DNA or RNA sequencing analysis. It has been cited in a number of publications [60, 81-84, 84].

Two Labome articles address the theoretical foundation and practical considerations of flow cytometry and FACS. Tree Star FlowJo and BD flow cytometry software dominate this area (Table 6).

The flow cytometry analysis involves manual organisation, analysis and report generation with the FCS files obtained from the flow cytometer. This analysis generally involves a large number of samples and FlowJo is a complete software that can help in all levels of analysis. Earlier in the process the software generates workspace templates saving sample organization time, analysis strategy and report output options. Thereafter FlowJo helps in batch analysis of samples, maintains consistency in the analysis for SOP, reduces downtime by eliminating manual analysis and report generation thereby increasing the laboratory capacity to handle high-throughput assays. FlowJo receives the files to be analyzed, performs auto-compensation by signal-processing and calculates gates and statistics before creating spreadsheets and graph reports. FlowJo can analyze data generated by any flow cytometer from any manufacturer.

FlowJo provides statistics from a large number of samples, which can be quickly generated, collated and exported. It can also perform specialized analyses such as DNA/Cell Cycle, Kinetics (Calcium flux), Proliferation, Calibration, and Statistical Comparison and presents output both in tabular and graphical format using sophisticated data presentation tools to generate publication quality material. The data is amenable for export to various formats ready to be analyzed by other packages or software. FlowJo follows a general workflow comprising of loading samples, grouping them with common procedures, analyzing simple prototype sample in detail to fix gating and statistics, applying appropriate analyses to all samples, verifying for the right gating for the samples analyzed, generating graphical output and finally the table with specific statistics from all samples. The package is one of the most complete and most cited software in this category, very little can be attributed to being against this software, which provides a great deal of user support and knowledge-base through its home page and blog.

For examples, TreeStar FlowJo software was used to analyze flow cytometry data to investigate the design of membraneless organelles for the incorporation of unnatural amino acids [89], the importance of the regulation of matrimony levels to the oocyte-to-embryo transition in Drosophila [90], the role of hybrid Th1/2 cells in natural immune responses against parasites [9], the importance of TCR signaling to natural killer T cell development [91], the regulatory role of Erf2 in protein palmitoylation and meiotic entry in Schizosaccharomyces pombe [28], the role of Lsd1 during blood cell maturation [92], the effect of JAK2 mutations on hematopoietic stem cells [93], the virus-induced evolution of transferrin receptor [94], the role of miR-146a in mouse hematopoietic stem cells [95], the different trafficking mechanisms of endosomal TLRs mediated by UNC93B1 [96], and the mechanism of immune evasion in cowpox virus [97]. Some articles cited FlowJo provided by BD as well [98, 99], such as FlowJo v10 [99].

CellQuest Pro, a proprietary software by BD Biosciences, allows a user to acquire and analyze data from a flow cytometer directly. It undertakes the quality checking measures like optimization of electronics for the samples by allowing FSC, SSC detector adjustment, gating for the population of interest and performing adjustments on detector and fluorescence compensation settings. The software acquires data and then displays them following which the analysis occurs. The data file contains the data with links or references for the analysed files and so the experiment document contains all files for plot, regions, gates, quadrant statistics, markers and annotated text but not the data files. The software provides a few graphing options like scatter, contour, and histogram. The user has to create histogram markers to generate statistics in the designated section of the diagram.

CellQuest Pro stays a minimalist tool that can perform a very basic level of analysis but is sufficient enough to arrive on conclusions. The limitation also extends to the features like import and export compatibility for external data types and production of publication quality images.

BD Biosciences CellQuest software, as examples, was used to analyze flow cytometry data to investigate the role of autophagy in the immunogenicity of antineoplastic chemotherapy in mice [100], the function of viperin in the infectious process [101], the role of BID, BIM, and PUMA in activating the BAX- and BAK-dependent cell death program [102].

FACSDiva, a product of BD Biosciences supporting its Flow Cytometry Analyzers and Sorters, is a collection of tools for application setup, data acquisition and data analysis to streamline the regular workflow in laboratories. They support multiple cytometers but are limited to those from BD, including 140 laser, mirror and filter combinations, standard gating types like interval, rectangle, hierarchical snap-to, quadrants and hinged quadrants and logical gating like And, Or, Not, Rest Of. The software can create experiments, plates and acquisition criteria from non-BD software. The data analysis can either be done manually or in batch using both standard and robust statistical tools and create plots, gates, population hierarchies and statistical views on a global worksheet.

A greater emphasis is laid for maintaining and obtaining consistency in data quality within the software set up. The Cytometer Setup and Tracking (CS&T) feature of BD FACSDiva helps set a baseline and adjust for instrument variability. The software helps reduce operator error by setting system time delay thereby ensuring consistency in results. The quality control tracking capabilities measure instrument setting and provide performance report. The Levey-Jennings plots help users understand instrument performance and identify maintenance issues.

BD Biosystem FACSdiva software was cited in the studies for G2/M checkpoint [103], blood vessels [12], blood-brain barrier [104], insect endosymbionts [105], HIV neutralizing antibodies [106], spinal cord injury [107], human long-term engrafting HSCs [108], influenza viruses [109], and tumor regression [110].

Gel and blot imaging software usually comes with the imaging instruments, except for ImageJ. Independent software includes "Densitometric Image Analysis Software", which evaluates the non-linearity of autoradiographic films during calibration and also calculates the protein-DNA binding constants from Electrophoretic Mobility Shift Assays [111].

LI-COR Biosciences Odyssey Infrared Imaging System is a popular choice for analyzing protein gel and Western blot images, for example, [86, 112].

Table 8 lists the major suppliers of microplate and microarray analysis software. Table 9 lists the major suppliers for mass spectrometry analysis software. Table 10 lists the major suppliers for electrophysiological recording and analysis software. Suppliers and their main brands for biochemical analyses are listed in Table 11.

Table 12 shows the main software used for image analysis. It can be used for many image modalities presented in that article, like cell and tissue imaging, flow cytometry or gel blot image analysis.

ImageJ is an open source software, that is continuously developed and improved with the help of NIH. It is freely available on common computational platforms like Windows, Linux and Mac and has a growing and engaging user community. It is designed with an open architecture, it is Java language based, offers numerous plugins and allows the creation of customized scripts (macros). It can be automated with macros from those that close all the open windows, copying data to clipboard, creating 3D spectrums, generic multicolor co-localization analysis to obtain volume fraction of bone, capture a sequence of time-lapse images as a stack and as days progress more and more of plugins of diverse nature meeting the demands of the user community. The software is very simple and can be used with any set of images taken for analysis. Though there is no separate module as such the simpler tools that are available can be categorized for user and developer software management. In image acquisition, support for almost all platforms has been made available to obtain input images. The analysis set comprises of many image analysis techniques both simple and advanced in nature. The pool of available filters like FFT filters that filters out large structures (shading correction) and small structures (smoothing) of the specified size by Gaussian filtering in Fourier space to rolling ball background subtraction that produces better results than the new ImageJ code for some 16-bit images. As seen from this filter whose disadvantage is in producing artifacts for many images if the ball radius is >=10 there is an inherent lack of completeness using one or following one method.

ImageJ’s disadvantages are its own advantages of being simple. The proprietary software could clear up the lacuna of one method by serially connecting another complementing method so as to minimize the problems in data analysis if not eradicate completely. So the ImageJ would lie as a better and more crisper tool for users who understand the method used unlike those found in proprietary software where its an easy click and save type of inbuilt calculations. Documentation plays an important role in ImageJ plugin creation and its feasibility depends on each developer willingness.

ImageJ and its bundled version Fiji [89, 117, 118], can be used to quantitate and process images from, for example, Western blot bands [119], immunocytochemical experiments [12, 23, 120-125], calcium live-cell images [119] and histological data [98]. Antón-Bolaños N et al used ImageJ to analyze axonal tracing data and calcium-fluorescent sensor data [126].

Icy is an open community platform for bioimage informatics that provides the software resources to visualize, annotate and quantify bioimaging data. The source code is directly available and provided in each application download. It is developed at Institut Pasteur. Like ImageJ it offers numerous plugins and allows the creation of customized scripts (macros).

CellProfiler is a free, open source software for quantitative analysis of biological images. Its development started in 2004 at Broad Institute [127]. No prior experience in programming or computer vision is required as it is easy to use. It allows to quantitatively measure phenotypes from thousands of images automatically.

Imaris (Bitplane) is a very intuitive and powerful software for visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. Apart from the powerful 3D visualization mode that we have seen above in that article, Imaris includes modules for analysis of filament structures, colocalization, particle tracking, measurement and statistics, data plotting, interpretation and mining and it offers the possibility of development of custom expansions in MATLAB and other programming languages.

Amira is a visualization and analysis software for 3D/4D data sets. It has been developed by Thermo Scientific. It is used for a range of image modalities, including CT, MRI, and 3D Light or Electron Microscopy.

Huygens Professional is an image processing software package, part of the Huygens Software, suitable for doing denoising and deconvolution of images. It contains powerful algorithms, compatible with GPU, for fast image analysis. It contains some analysis plugins, like object analyzer, colocalization analyzer or object tracking.

Ilastik is a simple, free, open source, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated pixel and object level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most operations are interactive, even on large datasets, one just needs to draw the labels and immediately see the result. It is developed in EMBL [128].

Adobe Photoshop is the only non-scientific software, but belongs to the expert area of art and design, in the entire set of software reviewed here. The tool is being used by the scientific community because of its ease in use, high-quality image processing and file format transferring ability of publication standards and editing for a qualitative purpose. For example, Szőnyi A et al counted the number of positive cells on confocal microscopic images of brain sections after immunohistochemical staining [117].

The disadvantage is the non-scientific nature as it supplements artistic quality improvement features rather than providing data acquisition or analysis tools.

The software being developed for a different target group it has been used for improving the image quality for scientific study with a note to bear that it lies on top of the chart of image analysis ahead of more scientific and industry-standard software supporting its popularity among the community to use Photoshop for science communication and research.

The articles in the reviewed dataset still can show their utility in areas very diverse as stem cells, neuronal development biology of the brain.

Matlab (MAathWorks) is a high-level language and interactive environment for numerical computation, visualization, and programming. The language, tools, and built-in math functions enable the user to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java.

Though there is a module or toolbox in Matlab that is associated for Biology, the Computational Biology Toolbox, interestingly none of the citations under this review had cited the use of this specific toolbox.

In the area of mathematical data analysis Matlab features one of the most exhaustive lists of possibilities in the way of looking at data. The four major areas of its capabilities are

1. Numeric Computation where one can use the built-in mathematical functions to solve the scientific problems.
2. Data Analysis and Visualization utilising which the data in its final format can be derived for conclusions and represented in terms of multidimensional graphs and different forms of graphs depending on the means to describe and express the interpretation. Here the data can be obtained by interacting with the hardware of diverse nature using appropriate add-ons thus fetching raw data, images, videos for analysis and visualisation.
3. Programming and Algorithm Development allows one to write codes in the native Matlab language or C, C++, Java, and .NET thus integrate Matlab applications with other languages. This helps utilize the full potential of Matlab to perform matrix and vector operations to solve scientific problems.
4. As a step towards the future, Matlab-based applications can be scripted and shared as code, executables or software tools thereby enabling the non-Matlab owners to utilize the potential of the code. The Graphical User Interface Development Environment can be used to make the users utilize the full potential of Matlab functions with a simple click of the mouse.

While the Computational ToolBox can help in areas like Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology studies and SimuLink software accompanying the main Matlab Software aids in systems biology studies, both are the exclusive software that can utilise the MatLab’s coding and algorithm base to enhance the quality of data.

Biologists have been increasingly affected by the use of computational tools like Matlab as they too can do some code writing depending on their needs. So Matlab has been a boon for such researchers who were having the ability to utilise electronic instruments alongside computers and derive lots of valuable interpretation on raw data analysis using Matlab and like programs. Hence the knowledge of basic mathematics, some coding skills are pre-requisite to utilize and broaden the practical limits of Matlab in biological research. For example, Antón-Bolaños N et al use Matlab routines to analyze In vivo extracellular electric recordings and thalamic calcium fluorescence data, and to conduct statistical analysis [126]. Szőnyi A et al also used custom-written functions and scripts in MATLAB environment to analyze In vivo electrophysiological recordings in freely behaving mice to study the role of brainstem nucleus incertus GABAergic cells in contextual memory formation [117].

Dr. Orestis Faklaris made substantial additions to the article, and was added as an author in October 2019.