Ion mobility mass spectrometry has become popular in proteomics lately, in particular because the Bruker timsTOF instruments have found significant adoption in proteomics facilities. The Bruker\'s implementation of the ion mobility dimension generates massive amounts of mass spectrometric data that require carefully designed software both to extract meaningful information and to perform processing tasks at reasonable speed. In a historical move, the Bruker company decided to harness the skills of the scientific software development community by releasing to the public the timsTOF data file format specification. As a proteomics facility that has been developing Free Open Source Software (FOSS) solutions since decades, we took advantage of this opportunity to implement the very first FOSS proteomics complete solution to natively read the timsTOF data, low-level process them, and explore them in an integrated quantitative proteomics software environment. We dubbed our software i2MassChroQ because it implements a (peptide)identification-(protein)inference-mass-chromatogram-quantification processing workflow. The software benchmarking results reported in this paper show that i2MassChroQ performed better than competing software on two critical characteristics: (1) feature extraction capability and (2) protein quantitative dynamic range. Altogether, i2MassChroQ yielded better quantified protein numbers, both in a technical replicate MS runs setting and in a differential protein abundance analysis setting.

Medical research uses increasingly massive, complex and interdependent data, the analysis of which requires the use of specialized algorithms. In order to independently reproduce and validate the results of a scientific study, it is no longer sufficient to share the text of the article as an open-access document, together with the raw research data according to the open-data approach. It is now also needed to share the algorithms used to analyze the data with other research teams. Free and open-source software precisely responds to this need to disseminate technical knowledge at a large scale. In this paper, we present several examples of free software used in medicine, with a particular focus on medical imaging.
La recherche médicale recourt à des données de plus en plus massives, complexes et interdépendantes dont l’analyse nécessite l’usage d’algorithmes spécialisés. Afin de reproduire et valider les résultats d’une étude scientifique de manière indépendante, il n’est, dès lors, plus suffisant de partager le texte de l’article en «open-access» complété avec les données brutes en «open-data». Il convient désormais d’également partager les algorithmes qui ont servi à l’analyse des données avec d’autres équipes de chercheurs. Le logiciel libre et «open-source» répond précisément à ce besoin de diffuser les connaissances techniques à grande échelle. Dans cet article, nous présentons plusieurs exemples de logiciels libres utilisés en médecine, avec une attention particulière portée à l’imagerie médicale.

OBJECTIVE: This study evaluated the segmentation accuracy and reliability of free software packages and compared them with commercial alternatives.
METHODS: A total of 36 stone models were scanned using a desktop scanner and then imaged by cone beam computed tomography (CBCT). The CBCT volumes were segmented using 2 free software packages (3D Slicer and Blue Sky Plan) and 2 commercial software packages (Mimics and OnDemand3D). Stereolithography (STL) files generated by the desktop scanner were used as the control group (reference models). The accuracy of segmentation was evaluated by (1) comparing 6 linear measurements taken from each STL model generated by the 4 software packages with that obtained by the scanner, and (2) deviation analysis of each STL model generated by the 4 software packages with that obtained by the scanner. Absolute error and percentage error, repeated measures anova and Friedman test followed by post hoc analysis, intraclass correlation coefficient (ICC), and Pearson\'s r were used to evaluate the accuracy of the tested software packages.
RESULTS: There was no statistically significant difference in all intra-arch measurements obtained using the four software packages. Measurements obtained using the free software packages and the scanner showed excellent positive correlation, ranging from 0.825 to 0.988, confirming equivalence with commercial software packages.
CONCLUSIONS: Within the settings of the current study, accurate and time-saving segmentations with high positive correlation could be performed using the tested free segmentation software packages (3D Slicer and Blue Sky Plan). Nevertheless, further evaluation is necessary to gage their accuracy using different CBCT modalities.

BACKGROUND: The vertical jump can be analyzed based on the flight time achieved by the individual. This measurement can be obtained using a force platform or a three-dimensional infrared camera system, but such equipment is expensive and requires training for data collection and processing. Thus, this study aimed to evaluate the accuracy and reliability of using a smartphone and the Kinovea software compared with a force platform as a method of vertical jump analysis.
METHODS: For this purpose, two independent evaluators analyzed videos of bipodal and unipodal vertical jumps by counting the variables among participants. The participants performed three consecutive jumps in bipodal and unipodal conditions with the dominant and non-dominant legs.
RESULTS: The intra-rater analysis for bipodal jumps was found to have excellent reproducibility (ICC = 0.903 to 0.934), whereas for unipodal jumps, the reproducibility was moderate to excellent (ICC = 0.713 to 0.902). The inter-rater analysis showed that for bipodal jumps, the reproducibility is substantial to excellent (ICC = 0.823 to 0.926), while for unipodal jumps, it is moderate (ICC = 0.554 to 0.702).
CONCLUSIONS: Therefore, it can be concluded that the vertical jump evaluation can be performed using the smartphone-Kinovea system. However, the same evaluator should carry out the evaluation to maintain reliable indices.

Surgical intervention for alveolar bone formation is important in patients with alveolar cleft; however, the treatment methods and materials are still controversial. A precise evaluation method for postoperative bone formation is important for comparing outcomes and establishing the best treatment protocol. The purpose of this study is to establish a new method of evaluating surgical outcomes for patients with alveolar cleft. Computed tomography datasets from 20 patients who underwent secondary alveolar bone grafting were obtained before and 1 year after surgery. Six anatomical landmarks were used to superimpose the preoperative and mirrored preoperative volume and postoperative volume data. The cleft region was segmented by subtracting the preoperative from mirrored preoperative volume data, and the failed osteogenesis region was segmented by subtracting the postoperative volume data from the cleft region; subsequently, the bone formation ratio was calculated. Two observers performed this method using a free software 3D slicer and the average evaluation times were 12.7 and 13.2 min for observers 1 and 2, respectively. Method reliability was determined by evaluating intraclass correlation coefficients. The intra-observer intraclass correlation coefficients were 0.97 and 0.96 for observers 1 and 2, respectively. The inter-observer intraclass correlation coefficient was 0.97. Our method is practical for assessing bone formation after treatment, which does not require specific knowledge or software and can be used by ordinary physicians.

When evaluating the impact of environmental exposures on human health, study designs often include a series of repeated measurements. The goal is to determine whether populations have different trajectories of the environmental exposure over time. Power analyses for longitudinal mixed models require multiple inputs, including clinically significant differences, standard deviations, and correlations of measurements. Further, methods for power analyses of longitudinal mixed models are complex and often challenging for the non-statistician. We discuss methods for extracting clinically relevant inputs from literature, and explain how to conduct a power analysis that appropriately accounts for longitudinal repeated measures. Finally, we provide careful recommendations for describing complex power analyses in a concise and clear manner.
For longitudinal studies of health outcomes from environmental exposures, we show how to [1] conduct a power analysis that aligns with the planned mixed model data analysis, [2] gather the inputs required for the power analysis, and [3] conduct repeated measures power analysis with a highly-cited, validated, free, point-and-click, web-based, open source software platform which was developed specifically for scientists.
As an example, we describe the power analysis for a proposed study of repeated measures of per- and polyfluoroalkyl substances (PFAS) in human blood. We show how to align data analysis and power analysis plan to account for within-participant correlation across repeated measures. We illustrate how to perform a literature review to find inputs for the power analysis. We emphasize the need to examine the sensitivity of the power values by considering standard deviations and differences in means that are smaller and larger than the speculated, literature-based values. Finally, we provide an example power calculation and a summary checklist for describing power and sample size analysis.
This paper provides a detailed roadmap for conducting and describing power analyses for longitudinal studies of environmental exposures. It provides a template and checklist for those seeking to write power analyses for grant applications.

Quality Control (QC) tests in mammography are very important, since mammograms have been used as a population-based screening test for more than 30 years and QCs lead to better image quality and radiation safety for patients. European guidelines, EUREF and EFOMP protocols provide comprehensive QC guidelines for digital mammography (DM) and digital breast tomosynthesis (DBT) units, respectively. We developed a novel, fast, free and platform independent software (named MAMMO_QC) for QC performance tests in DM and tomosynthesis, based on the aforementioned guidelines. MAMMO_QC consists of a series of ImageJ plugins for DM and DBT. It does not require any programming knowledge and can be used to evaluate several performance parameters, such as pre-sampled modulation transfer function (pMTF), normalised noise power spectrum (NNPS), detective quantum efficiency (DQE), contrast-detail analysis based on the CDMAM 3.4 and 4.0 test tools, homogeneity and artefacts, automatic exposure control (AEC) performance. The user can use MAMMO_QC for acceptance, commissioning and routine QC performance analysis based on the European guidelines. We validated our results against well-established software products used in mammography and DBT (i.e., COQ, OBJ_IQ_reduced and Artinis CDMAM Analyzer). All the average relative differences were within 5.5%, and several years of usage and testing allows us to consider MAMMO_QC as an accurate and reliable tool for QC on DM and DBT systems. Our developed software for DM and DBT computes almost all the parameters stated in the European, EUREF and EFOMP guidelines. To the best of our knowledge, no such software has been developed so far.

In the field of biology, and specifically in protein and peptide science, the power of mass spectrometry is that it is applicable to a vast spectrum of applications. Mass spectrometry can be applied to identify proteins and peptides in complex mixtures, to identify and locate post-translational modifications, to characterize the structure of proteins and peptides to the most detailed level or to detect protein-ligand non-covalent interactions. Thanks to the Free and Open Source Software (FOSS) movement, scientists have limitless opportunities to deepen their skills in software development to code software that solves mass spectrometric data analysis problems. After the conversion of raw data files into open standard format files, the entire spectrum of data analysis tasks can now be performed integrally on FOSS platforms, like GNU/Linux, and only with FOSS solutions. This review presents a brief history of mass spectrometry open file formats and goes on with the description of FOSS projects that are commonly used in protein and peptide mass spectrometry fields of endeavor: identification projects that involve mostly automated pipelines, like proteomics and peptidomics, and bio-structural characterization projects that most often involve manual scrutiny of the mass data. Projects of the last kind usually involve software that allows the user to delve into the mass data in an interactive graphics-oriented manner. Software projects are thus categorized on the basis of these criteria: software libraries for software developers vs desktop-based graphical user interface, software for the end-user and automated pipeline-based data processing vs interactive graphics-based mass data scrutiny.

UNASSIGNED: Considering the need for daily activity analysis of older adults, development of easy-to-use, free electroencephalogram (EEG) analysis tools are desired in order to decrease barriers to accessing this technology and increase the entry of a wide range of new researchers.
UNASSIGNED: We describe a newly developed tool set for EEG analysis, enabling import, average, waveform display and iso-potential scalp topographies, utilizing the programming language Perl.
UNASSIGNED: The basic processing, including average, display waveforms, and isopotential scalp topography was implemented in the current system. The validation was examined by making difference waveforms between the results using the current analysis system and a commercial software.Comparison with Existing Method(s): The current software tool set consists of free software. The scripts are easily editable by any user and there are no black boxes.
UNASSIGNED: The currently reported procedures provide an easy-to-begin, flexible, readable, easy-to-modify basic tool set for EEG analysis and is expected to recruit new EEG researchers.

The purpose of this technical note is to illustrate a simple and economical preoperative method for preshaping a reconstructive titanium plate in a fibula free flap (FFF) by using 3D printing of a virtually reconstructed mandible haptic model. The whole process consisted in creating a 3D model of the patient\'s mandible based on a CT-scan using a combination of free software (3Dslicer and ITK-snap), and simulating the surgical osteotomies and reconstruction, and print it as a guide for bending a reconstruction titanium plate. Reconstruction is performed using virtual cubes (1 to 3 cubes, according the number of FFF osteotomies). This virtual lab work is performed using 3D Builder® (Microsoft, Redmond) software. This technique allows obtaining an optimal plate application on the bony fragments. It facilitates reconstructive surgery with good functional (putting the patient back in an optimal dental occlusion based on the native maxilla) and aesthetic results. This technical note presents a simple and economical preoperative fabrication of a reconstructive plate through freeware and a low-cost 3D printer accessible to all surgeons.