@MISC{European_Organization_for_Nuclear_Research2013-uf,

title = "Zenodo",

author = "{European Organization for Nuclear Research} and {OpenAIRE}",

abstract = "Zenodo is a general purpose repository that enables researchers,

scientists, projects and institutions to share, preserve and

showcase multidisciplinary research results (data, software and

publications) that are not part of the existing institutional or

subject-based repositories of the research communities. It is

founded in the trustworthy CERN data centre.",

publisher = "CERN",

year = 2013

}

@ARTICLE{Brown2007-ou,

title = "Fluorescence microscopy--avoiding the pitfalls",

author = "Brown, Claire M",

journal = "J. Cell Sci.",

volume = 120,

number = "Pt 10",

pages = "1703--1705",

month = may,

year = 2007,

language = "en"

}

@MISC{noauthor_undated-tk,

title = "{OSF}",

howpublished = "\url{https://osf.io/}",

note = "Accessed: 2022-12-14",

language = "en"

}

@ARTICLE{Culley2023-dj,

title = "Made to measure: an introduction to quantification in

microscopy data",

author = "Culley, Si{\^a}n and Caballero, Alicia Cuber and Burden,

Jemima J and Uhlmann, Virginie",

abstract = "Images are at the core of most modern biological experiments

and are used as a major source of quantitative information.

Numerous algorithms are available to process images and make

them more amenable to be measured. Yet the nature of the

quantitative output that is useful for a given biological

experiment is uniquely dependent upon the question being

investigated. Here, we discuss the 3 main types of visual

information that can be extracted from microscopy data:

intensity, morphology, and object counts or categorical

labels. For each, we describe where they come from, how they

can be measured, and what may affect the relevance of these

measurements in downstream data analysis. Acknowledging that

what makes a measurement ``good'' is ultimately down to the

biological question being investigated, this review aims at

providing readers with a toolkit to challenge how they

quantify their own data and be critical of conclusions drawn

from quantitative bioimage analysis experiments.",

month = feb,

year = 2023,

archivePrefix = "arXiv",

journal = "arxiv",

primaryClass = "q-bio.QM",

eprint = "2302.01657"

}

@ARTICLE{Pittet2011-dn,

title = "Intravital imaging",

author = "Pittet, Mikael J and Weissleder, Ralph",

abstract = "Until recently, the idea of observing life deep within the

tissues of a living mouse, at a resolution sufficient to pick out

cellular behaviors and molecular signals underlying them,

remained a much-coveted dream. Now, a new era of intravital

fluorescence microscopy has dawned. In this Primer, we review the

technologies that made this revolution possible and demonstrate

how intravital imaging is beginning to provide quantitative and

dynamic insights into cell biology, immunology, tumor biology,

and neurobiology.",

journal = "Cell",

volume = 147,

number = 5,

pages = "983--991",

month = nov,

year = 2011,

language = "en"

}

@ARTICLE{Ellenberg2018-co,

title = "A call for public archives for biological image data",

author = "Ellenberg, Jan and Swedlow, Jason R and Barlow, Mary and Cook,

Charles E and Sarkans, Ugis and Patwardhan, Ardan and Brazma,

Alvis and Birney, Ewan",

abstract = "Public data archives are the backbone of modern biological

research. Biomolecular archives are well established, but

bioimaging resources lag behind them. The technology required for

imaging archives is now available, thus enabling the creation of

the first public bioimage datasets. We present the rationale for

the construction of bioimage archives and their associated

databases to underpin the next revolution in bioinformatics

discovery.",

journal = "Nat. Methods",

volume = 15,

number = 11,

pages = "849--854",

month = nov,

year = 2018,

language = "en"

}

@ARTICLE{Soneson2014-hw,

title = "Batch effect confounding leads to strong bias in performance

estimates obtained by cross-validation",

author = "Soneson, Charlotte and Gerster, Sarah and Delorenzi, Mauro",

abstract = "BACKGROUND: With the large amount of biological data that is

currently publicly available, many investigators combine multiple

data sets to increase the sample size and potentially also the

power of their analyses. However, technical differences (``batch

effects'') as well as differences in sample composition between

the data sets may significantly affect the ability to draw

generalizable conclusions from such studies. FOCUS: The current

study focuses on the construction of classifiers, and the use of

cross-validation to estimate their performance. In particular, we

investigate the impact of batch effects and differences in sample

composition between batches on the accuracy of the classification

performance estimate obtained via cross-validation. The focus on

estimation bias is a main difference compared to previous

studies, which have mostly focused on the predictive performance

and how it relates to the presence of batch effects. DATA: We

work on simulated data sets. To have realistic intensity

distributions, we use real gene expression data as the basis for

our simulation. Random samples from this expression matrix are

selected and assigned to group 1 (e.g., 'control') or group 2

(e.g., 'treated'). We introduce batch effects and select some

features to be differentially expressed between the two groups.

We consider several scenarios for our study, most importantly

different levels of confounding between groups and batch effects.

METHODS: We focus on well-known classifiers: logistic regression,

Support Vector Machines (SVM), k-nearest neighbors (kNN) and

Random Forests (RF). Feature selection is performed with the

Wilcoxon test or the lasso. Parameter tuning and feature

selection, as well as the estimation of the prediction

performance of each classifier, is performed within a nested

cross-validation scheme. The estimated classification performance

is then compared to what is obtained when applying the classifier

to independent data.",

journal = "PLoS One",

volume = 9,

number = 6,

pages = "e100335",

month = jun,

year = 2014,

language = "en"

}

@ARTICLE{Hartley2022-mt,

title = "The {BioImage} Archive - Building a Home for {Life-Sciences}

Microscopy Data",

author = "Hartley, Matthew and Kleywegt, Gerard J and Patwardhan, Ardan and

Sarkans, Ugis and Swedlow, Jason R and Brazma, Alvis",

abstract = "Despite the huge impact of data resources in genomics and

structural biology, until now there has been no central archive

for biological data for all imaging modalities. The BioImage

Archive is a new data resource at the European Bioinformatics

Institute (EMBL-EBI) designed to fill this gap. In its initial

development BioImage Archive accepts bioimaging data associated

with publications, in any format, from any imaging modality from

the molecular to the organism scale, excluding medical imaging.

The BioImage Archive will ensure reproducibility of published

studies that derive results from image data and reduce

duplication of effort. Most importantly, the BioImage Archive

will help scientists to generate new insights through reuse of

existing data to answer new biological questions, and provision

of training, testing and benchmarking data for development of

tools for image analysis. The archive is available at

https://www.ebi.ac.uk/bioimage-archive/.",

journal = "J. Mol. Biol.",

volume = 434,

number = 11,

pages = "167505",

month = jun,

year = 2022,

keywords = "FAIR; database; imaging; microscopy; open",

language = "en"

}

@ARTICLE{Icha2017-jf,

title = "Phototoxicity in live fluorescence microscopy, and how to avoid

it",

author = "Icha, Jaroslav and Weber, Michael and Waters, Jennifer C and

Norden, Caren",

abstract = "Phototoxicity frequently occurs during live fluorescence

microscopy, and its consequences are often underestimated. Damage

to cellular macromolecules upon excitation light illumination can

impair sample physiology, and even lead to sample death. In this

review, we explain how phototoxicity influences live samples, and

we highlight that, besides the obvious effects of phototoxicity,

there are often subtler consequences of illumination that are

imperceptible when only the morphology of samples is examined.

Such less apparent manifestations of phototoxicity are equally

problematic, and can change the conclusions drawn from an

experiment. Thus, limiting phototoxicity is a prerequisite for

obtaining reproducible quantitative data on biological processes.

We present strategies to reduce phototoxicity, e.g. limiting the

illumination to the focal plane and suggest controls for

phototoxicity effects. Overall, we argue that phototoxicity needs

increased attention from researchers when designing experiments,

and when evaluating research findings.",

journal = "Bioessays",

volume = 39,

number = 8,

month = aug,

year = 2017,

keywords = "light sheet fluorescence microscopy; live imaging;

photobleaching; photodamage; phototoxicity; reactive oxygen

species; selective plane illumination",

language = "en"

}

@ARTICLE{Li2015-ys,

title = "Paraformaldehyde Fixation May Lead to Misinterpretation of the

Subcellular Localization of Plant High Mobility Group Box

Proteins",

author = "Li, Man-Wah and Zhou, Liang and Lam, Hon-Ming",

abstract = "Arabidopsis High Mobility Group Box (HMBG) proteins were

previously found associated with the interphase chromatin but not

the metaphase chromosome. However, these studies are usually

based on immunolocalization analysis involving paraformaldehyde

fixation. Paraformaldehyde fixation has been widely adapted to

preserved cell morphology before immunofluorescence staining. On

one hand, the processed cells are no longer living. On the other

hand, the processing may lead to misinterpretation of

localization. HMGBs from Arabidopsis were fused with enhanced

green fluorescence protein (EGFP) and transformed into tobacco

BY-2 cells. Basically, the localization of these HMGB proteins

detected with EGFP fluorescence in interphase agreed with

previous publications. Upon 4\% paraformaldehyde fixation,

AtHMGB1 was found associated with interphase but not the

metaphase chromosomes as previously reported. However, when EGFP

fluorescence signal was directly observed under confocal

microscope without fixation, association of AtHMGB1 with

metaphase chromosomes can be detected. Paraformaldehyde fixation

led to dissociation of EGFP tagged AtHMBG1 protein from metaphase

chromosomes. This kind of pre-processing of live specimen may

lead to dissociation of protein-protein or protein-nucleic acid

interaction. Therefore, using of EGFP fusion proteins in live

specimen is a better way to determine the correct localization

and interaction of proteins.",

journal = "PLoS One",

volume = 10,

number = 8,

pages = "e0135033",

month = aug,

year = 2015,

language = "en"

}

@ARTICLE{Schindelin2012-kk,

title = "Fiji: an open-source platform for biological-image analysis",

author = "Schindelin, Johannes and Arganda-Carreras, Ignacio and Frise,

Erwin and Kaynig, Verena and Longair, Mark and Pietzsch, Tobias

and Preibisch, Stephan and Rueden, Curtis and Saalfeld, Stephan

and Schmid, Benjamin and Tinevez, Jean-Yves and White, Daniel

James and Hartenstein, Volker and Eliceiri, Kevin and Tomancak,

Pavel and Cardona, Albert",

abstract = "Fiji is a distribution of the popular open-source software ImageJ

focused on biological-image analysis. Fiji uses modern software

engineering practices to combine powerful software libraries with

a broad range of scripting languages to enable rapid prototyping

of image-processing algorithms. Fiji facilitates the

transformation of new algorithms into ImageJ plugins that can be

shared with end users through an integrated update system. We

propose Fiji as a platform for productive collaboration between

computer science and biology research communities.",

journal = "Nat. Methods",

volume = 9,

number = 7,

pages = "676--682",

month = jun,

year = 2012,

language = "en"

}

@ARTICLE{Gomez-Gaviro2020-jq,

title = "Biomedical Applications of Tissue Clearing and

{Three-Dimensional} Imaging in Health and Disease",

author = "G{\'o}mez-Gaviro, Maria Victoria and Sanderson, Daniel and

Ripoll, Jorge and Desco, Manuel",

abstract = "Three-dimensional (3D) optical imaging techniques can expand our

knowledge about physiological and pathological processes that

cannot be fully understood with 2D approaches. Standard

diagnostic tests frequently are not sufficient to unequivocally

determine the presence of a pathological condition. Whole-organ

optical imaging requires tissue transparency, which can be

achieved by using tissue clearing procedures enabling deeper

image acquisition and therefore making possible the analysis of

large-scale biological tissue samples. Here, we review currently

available clearing agents, methods, and their application in

imaging of physiological or pathological conditions in different

animal and human organs. We also compare different optical tissue

clearing methods discussing their advantages and disadvantages

and review the use of different 3D imaging techniques for the

visualization and image acquisition of cleared tissues. The use

of optical tissue clearing resources for large-scale biological

tissues 3D imaging paves the way for future applications in

translational and clinical research.",

journal = "iScience",

volume = 23,

number = 8,

pages = "101432",

month = aug,

year = 2020,

keywords = "Biomedical Discipline; Imaging Methods in Chemistry; Medical

Imaging; Optical Imaging",

language = "en"

}

@ARTICLE{Stirling2021-sg,

title = "{CellProfiler} 4: improvements in speed, utility and usability",

author = "Stirling, David R and Swain-Bowden, Madison J and Lucas, Alice M

and Carpenter, Anne E and Cimini, Beth A and Goodman, Allen",

abstract = "BACKGROUND: Imaging data contains a substantial amount of

information which can be difficult to evaluate by eye. With the

expansion of high throughput microscopy methodologies producing

increasingly large datasets, automated and objective analysis of

the resulting images is essential to effectively extract

biological information from this data. CellProfiler is a free,

open source image analysis program which enables researchers to

generate modular pipelines with which to process microscopy

images into interpretable measurements. RESULTS: Herein we

describe CellProfiler 4, a new version of this software with

expanded functionality. Based on user feedback, we have made

several user interface refinements to improve the usability of

the software. We introduced new modules to expand the

capabilities of the software. We also evaluated performance and

made targeted optimizations to reduce the time and cost

associated with running common large-scale analysis pipelines.

CONCLUSIONS: CellProfiler 4 provides significantly improved

performance in complex workflows compared to previous versions.

This release will ensure that researchers will have continued

access to CellProfiler's powerful computational tools in the

coming years.",

journal = "BMC Bioinformatics",

volume = 22,

number = 1,

pages = "433",

month = sep,

year = 2021,

keywords = "Bioimaging; Image analysis; Image quantitation; Image

segmentation; Microscopy",

language = "en"

}

@ARTICLE{Wan2019-rv,

title = "{Light-Sheet} Microscopy and Its Potential for Understanding

Developmental Processes",

author = "Wan, Yinan and McDole, Katie and Keller, Philipp J",

abstract = "The ability to visualize and quantitatively measure dynamic

biological processes in vivo and at high spatiotemporal

resolution is of fundamental importance to experimental

investigations in developmental biology. Light-sheet microscopy

is particularly well suited to providing such data, since it

offers exceptionally high imaging speed and good spatial

resolution while minimizing light-induced damage to the specimen.

We review core principles and recent advances in light-sheet

microscopy, with a focus on concepts and implementations relevant

for applications in developmental biology. We discuss how

light-sheet microcopy has helped advance our understanding of

developmental processes from single-molecule to whole-organism

studies, assess the potential for synergies with other

state-of-the-art technologies, and introduce methods for

computational image and data analysis. Finally, we explore the

future trajectory of light-sheet microscopy, discuss key efforts

to disseminate new light-sheet technology, and identify exciting

opportunities for further advances.",

journal = "Annu. Rev. Cell Dev. Biol.",

volume = 35,

pages = "655--681",

month = oct,

year = 2019,

keywords = "cellular dynamics; embryonic development; fluorescence

microscopy; image processing; light-sheet microscopy; live

imaging",

language = "en"

}

@ARTICLE{Tosheva2020-wq,

title = "Between life and death: strategies to reduce phototoxicity in

super-resolution microscopy",

author = "Tosheva, Kalina L and Yuan, Yue and Matos Pereira, Pedro and

Culley, Si{\^a}n and Henriques, Ricardo",

abstract = "Super-resolution microscopy (SRM) enables non-invasive,

molecule-specific imaging of the internal structure and dynamics

of cells with sub-diffraction limit spatial resolution. One of

its major limitations is the requirement for high-intensity

illumination, generating considerable cellular phototoxicity.

This factor considerably limits the capacity for live-cell

observations, particularly for extended periods of time. Here, we

give an overview of new developments in hardware, software and

probe chemistry aiming to reduce phototoxicity. Additionally, we

discuss how the choice of biological model and sample environment

impacts the capacity for live-cell observations.",

journal = "J. Phys. D Appl. Phys.",

volume = 53,

number = 16,

pages = "163001",

month = apr,

year = 2020,

keywords = "fluorescence; photodamage; phototoxicity; super-resolution

microscopy",

language = "en"

}

@BOOK{Fay2018-mn,

title = "A biologist's guide to statistical thinking and analysis",

author = "Fay, David S and Gerow, Ken",

abstract = "The proper understanding and use of statistical tools are

essential to the scientific enterprise. This is true both at the

level of designing one's own experiments as well as for

critically evaluating studies carried out by others.

Unfortunately, many researchers who are otherwise rigorous and

thoughtful in their scientific approach lack sufficient

knowledge of this field. This methods chapter is written with

such individuals in mind. Although the majority of examples are

drawn from the field of Caenorhabditis elegans biology, the

concepts and practical applications are also relevant to those

who work in the disciplines of molecular genetics and cell and

developmental biology. Our intent has been to limit theoretical

considerations to a necessary minimum and to use common examples

as illustrations for statistical analysis. Our chapter includes

a description of basic terms and central concepts and also

contains in-depth discussions on the analysis of means,

proportions, ratios, probabilities, and correlations. We also

address issues related to sample size, normality, outliers, and

non-parametric approaches.",

publisher = "WormBook",

year = 2018

}

@ARTICLE{Stemmer2008-ua,

title = "Widefield fluorescence microscopy with extended resolution",

author = "Stemmer, Andreas and Beck, Markus and Fiolka, Reto",

abstract = "Widefield fluorescence microscopy is seeing dramatic improvements

in resolution, reaching today 100 nm in all three dimensions.

This gain in resolution is achieved by dispensing with uniform

K{\"o}hler illumination. Instead, non-uniform excitation light

patterns with sinusoidal intensity variations in one, two, or

three dimensions are applied combined with powerful image

reconstruction techniques. Taking advantage of non-linear

fluorophore response to the excitation field, the resolution can

be further improved down to several 10 nm. In this review

article, we describe the image formation in the microscope and

computational reconstruction of the high-resolution dataset when

exciting the specimen with a harmonic light pattern conveniently

generated by interfering laser beams forming standing waves. We

will also discuss extensions to total internal reflection

microscopy, non-linear microscopy, and three-dimensional imaging.",

journal = "Histochem. Cell Biol.",

volume = 130,

number = 5,

pages = "807--817",

month = nov,

year = 2008,

language = "en"

}

@ARTICLE{Halchenko2021-nd,

title = "{DataLad}: distributed system for joint management of code,

data, and their relationship",

author = "Halchenko, Yaroslav and Meyer, Kyle and Poldrack, Benjamin and

Solanky, Debanjum and Wagner, Adina and Gors, Jason and

MacFarlane, Dave and Pustina, Dorian and Sochat, Vanessa and

Ghosh, Satrajit and M{\"o}nch, Christian and Markiewicz,

Christopher and Waite, Laura and Shlyakhter, Ilya and de la

Vega, Alejandro and Hayashi, Soichi and H{\"a}usler, Christian

and Poline, Jean-Baptiste and Kadelka, Tobias and Skyt{\'e}n,

Kusti and Jarecka, Dorota and Kennedy, David and Strauss, Ted

and Cieslak, Matt and Vavra, Peter and Ioanas, Horea-Ioan and

Schneider, Robin and Pfl{\"u}ger, Mika and Haxby, James and

Eickhoff, Simon and Hanke, Michael",

journal = "J. Open Source Softw.",

publisher = "The Open Journal",

volume = 6,

number = 63,

pages = "3262",

month = jul,

year = 2021,

copyright = "http://creativecommons.org/licenses/by/4.0/"

}

@ARTICLE{Sanderson2014-ea,

title = "Fluorescence microscopy",

author = "Sanderson, Michael J and Smith, Ian and Parker, Ian and Bootman,

Martin D",

abstract = "Fluorescence microscopy is a major tool with which to monitor

cell physiology. Although the concepts of fluorescence and its

optical separation using filters remain similar, microscope

design varies with the aim of increasing image contrast and

spatial resolution. The basics of wide-field microscopy are

outlined to emphasize the selection, advantages, and correct use

of laser scanning confocal microscopy, two-photon microscopy,

scanning disk confocal microscopy, total internal reflection, and

super-resolution microscopy. In addition, the principles of how

these microscopes form images are reviewed to appreciate their

capabilities, limitations, and constraints for operation.",

journal = "Cold Spring Harb. Protoc.",

volume = 2014,

number = 10,

pages = "db.top071795",

month = oct,

year = 2014,

language = "en"

}

@ARTICLE{Irgen-Gioro2022-gu,

title = "Fixation can change the appearance of phase separation in living

cells",

author = "Irgen-Gioro, Shawn and Yoshida, Shawn and Walling, Victoria and

Chong, Shasha",

abstract = "Fixing cells with paraformaldehyde (PFA) is an essential step in

numerous biological techniques as it is thought to preserve a

snapshot of biomolecular transactions in living cells. Fixed-cell

imaging techniques such as immunofluorescence have been widely

used to detect liquid-liquid phase separation (LLPS) in vivo.

Here, we compared images, before and after fixation, of cells

expressing intrinsically disordered proteins that are able to

undergo LLPS. Surprisingly, we found that PFA fixation can both

enhance and diminish putative LLPS behaviors. For specific

proteins, fixation can even cause their droplet-like puncta to

artificially appear in cells that do not have any detectable

puncta in the live condition. Fixing cells in the presence of

glycine, a molecule that modulates fixation rates, can reverse

the fixation effect from enhancing to diminishing LLPS

appearance. We further established a kinetic model of fixation in

the context of dynamic protein-protein interactions. Simulations

based on the model suggest that protein localization in fixed

cells depends on an intricate balance of protein-protein

interaction dynamics, the overall rate of fixation, and notably,

the difference between fixation rates of different proteins.

Consistent with simulations, live-cell single-molecule imaging

experiments showed that a fast overall rate of fixation relative

to protein-protein interaction dynamics can minimize fixation

artifacts. Our work reveals that PFA fixation changes the

appearance of LLPS from living cells, presents a caveat in

studying LLPS using fixation-based methods, and suggests a

mechanism underlying the fixation artifact.",

journal = "Elife",

volume = 11,

month = nov,

year = 2022,

keywords = "cell biology; cross-linking; fixation; intrinsically disordered

proteins; liquid--liquid phase separation; live-cell

single-molecule imaging; multivalent protein--protein

interactions; none; paraformaldehyde; physics of living systems",

language = "en"

}

@ARTICLE{Neyman1928-mx,

title = "{ON} {THE} {USE} {AND} {INTERPRETATION} {OF} {CERTAIN} {TEST}

{CRITERIA} {FOR} {PURPOSES} {OF} {STATISTICAL} {INFERENCE}",

author = "Neyman, J and Pearson, E S",

abstract = "J. NEYMAN, PH.D., E. S. PEARSON, D.Sc.; ON THE USE AND

INTERPRETATION OF CERTAIN TEST CRITERIA FOR PURPOSES OF

STATISTICAL INFERENCE, Biometrika, Volume 20A, Is",

journal = "Biometrika",

publisher = "Oxford Academic",

volume = "20A",

number = "3-4",

pages = "263--294",

month = dec,

year = 1928

}

@ARTICLE{Schneider2012-gs,

title = "{NIH} Image to {ImageJ}: 25 years of image analysis",

author = "Schneider, Caroline A and Rasband, Wayne S and Eliceiri, Kevin W",

abstract = "For the past 25 years NIH Image and ImageJ software have been

pioneers as open tools for the analysis of scientific images. We

discuss the origins, challenges and solutions of these two

programs, and how their history can serve to advise and inform

other software projects.",

journal = "Nat. Methods",

volume = 9,

number = 7,

pages = "671--675",

month = jul,

year = 2012,

language = "en"

}

@MISC{Kenneth_R_Spring_Hiroshi_Komatsu_Martin_L_Scott_Stanley_A_Schwartz_Thomas_J_Fellers_Kathleen_E_Carr_Matthew_Parry-Hill_Michael_W_Davidson_undated-md,

title = "Basic Concepts and Formulas in Microscopy",

booktitle = "Nikon's {MicroscopyU}",

author = "{Kenneth R. Spring, Hiroshi Komatsu, Martin L. Scott ,

Stanley A. Schwartz, Thomas J. Fellers, Kathleen E. Carr,

Matthew Parry-Hill, Michael W. Davidson}",

abstract = "A thorough understanding of the concepts and formulas in

optical microscopy is essential in obtaining maximum

performance of the instrument.",

howpublished = "\url{https://www.microscopyu.com/microscopy-basics}",

note = "Accessed: NA-NA-NA"

}

@ARTICLE{Bauch2011-wi,

title = "{openBIS}: a flexible framework for managing and analyzing

complex data in biology research",

author = "Bauch, Angela and Adamczyk, Izabela and Buczek, Piotr and Elmer,

Franz-Josef and Enimanev, Kaloyan and Glyzewski, Pawel and

Kohler, Manuel and Pylak, Tomasz and Quandt, Andreas and

Ramakrishnan, Chandrasekhar and Beisel, Christian and

Malmstr{\"o}m, Lars and Aebersold, Ruedi and Rinn, Bernd",

abstract = "BACKGROUND: Modern data generation techniques used in distributed

systems biology research projects often create datasets of

enormous size and diversity. We argue that in order to overcome

the challenge of managing those large quantitative datasets and

maximise the biological information extracted from them, a sound

information system is required. Ease of integration with data

analysis pipelines and other computational tools is a key

requirement for it. RESULTS: We have developed openBIS, an open

source software framework for constructing user-friendly,

scalable and powerful information systems for data and metadata

acquired in biological experiments. openBIS enables users to

collect, integrate, share, publish data and to connect to data

processing pipelines. This framework can be extended and has been

customized for different data types acquired by a range of

technologies. CONCLUSIONS: openBIS is currently being used by

several SystemsX.ch and EU projects applying mass spectrometric

measurements of metabolites and proteins, High Content Screening,

or Next Generation Sequencing technologies. The attributes that

make it interesting to a large research community involved in

systems biology projects include versatility, simplicity in

deployment, scalability to very large data, flexibility to handle

any biological data type and extensibility to the needs of any

research domain.",

journal = "BMC Bioinformatics",

volume = 12,

pages = "468",

month = dec,

year = 2011,

language = "en"

}

@ARTICLE{Krishnamurthy2019-fk,

title = "Ex Vivo Microscopy: A Promising {Next-Generation} Digital

Microscopy Tool for Surgical Pathology Practice",

author = "Krishnamurthy, Savitri and Brown, Jonathan Quincy and Iftimia,

Nicusor and Levenson, Richard M and Rajadhyaksha, Milind",

abstract = "CONTEXT.---: The rapid evolution of optical imaging modalities in

recent years has opened the opportunity for ex vivo tissue

imaging, which has significant implications for surgical

pathology practice. These modalities have promising potential to

be used as next-generation digital microscopy tools for

examination of fresh tissue, with or without labeling with

contrast agents. OBJECTIVE.---: To review the literature

regarding various types of ex vivo optical imaging platforms that

can generate digital images for tissue recognition with potential

for utilization in anatomic pathology clinical practices. DATA

SOURCES.---: Literature relevant to ex vivo tissue imaging

obtained from the PubMed database. CONCLUSIONS.---: Ex vivo

imaging of tissues can be performed by using various types of

optical imaging techniques. These next-generation digital

microscopy tools have a promising potential for utilization in

surgical pathology practice.",

journal = "Arch. Pathol. Lab. Med.",

volume = 143,

number = 9,

pages = "1058--1068",

month = sep,

year = 2019,

language = "en"

}

@ARTICLE{Rossner2004-be,

title = "What's in a picture? The temptation of image manipulation",

author = "Rossner, Mike and Yamada, Kenneth M",

journal = "J. Cell Biol.",

volume = 166,

number = 1,

pages = "11--15",

month = jul,

year = 2004,

language = "en"

}

@ARTICLE{Lord2020-sp,

title = "{SuperPlots}: Communicating reproducibility and variability in

cell biology",

author = "Lord, Samuel J and Velle, Katrina B and Mullins, R Dyche and

Fritz-Laylin, Lillian K",

abstract = "P values and error bars help readers infer whether a reported

difference would likely recur, with the sample size n used for

statistical tests representing biological replicates, independent

measurements of the population from separate experiments. We

provide examples and practical tutorials for creating figures

that communicate both the cell-level variability and the

experimental reproducibility.",

journal = "J. Cell Biol.",

volume = 219,

number = 6,

month = jun,

year = 2020,

language = "en"

}

@ARTICLE{Uhlen2016-wy,

title = "A proposal for validation of antibodies",

author = "Uhlen, Mathias and Bandrowski, Anita and Carr, Steven and

Edwards, Aled and Ellenberg, Jan and Lundberg, Emma and Rimm,

David L and Rodriguez, Henry and Hiltke, Tara and Snyder, Michael

and Yamamoto, Tadashi",

journal = "Nat. Methods",

volume = 13,

number = 10,

pages = "823--827",

month = oct,

year = 2016,

language = "en"

}

% The entry below contains non-ASCII chars that could not be converted

% to a LaTeX equivalent.

@ARTICLE{Shapiro1965-xf,

title = "An analysis of variance test for normality (complete samples)",

author = "Shapiro, S S and Wilk, M B",

abstract = "S. S. SHAPIRO, M. B. WILK; An analysis of variance test for

normality (complete samples)†, Biometrika, Volume 52, Issue 3-4,

1 December 1965, Pages 591--611, htt",

journal = "Biometrika",

publisher = "Oxford Academic",

volume = 52,

number = "3-4",

pages = "591--611",

month = dec,

year = 1965

}

@ARTICLE{Rueden2017-ku,

title = "{ImageJ2}: {ImageJ} for the next generation of scientific image

data",

author = "Rueden, Curtis T and Schindelin, Johannes and Hiner, Mark C and

DeZonia, Barry E and Walter, Alison E and Arena, Ellen T and

Eliceiri, Kevin W",

abstract = "BACKGROUND: ImageJ is an image analysis program extensively used

in the biological sciences and beyond. Due to its ease of use,

recordable macro language, and extensible plug-in architecture,

ImageJ enjoys contributions from non-programmers, amateur

programmers, and professional developers alike. Enabling such a

diversity of contributors has resulted in a large community that

spans the biological and physical sciences. However, a rapidly

growing user base, diverging plugin suites, and technical

limitations have revealed a clear need for a concerted software

engineering effort to support emerging imaging paradigms, to

ensure the software's ability to handle the requirements of

modern science. RESULTS: We rewrote the entire ImageJ codebase,

engineering a redesigned plugin mechanism intended to facilitate

extensibility at every level, with the goal of creating a more

powerful tool that continues to serve the existing community

while addressing a wider range of scientific requirements. This

next-generation ImageJ, called ``ImageJ2'' in places where the

distinction matters, provides a host of new functionality. It

separates concerns, fully decoupling the data model from the user

interface. It emphasizes integration with external applications

to maximize interoperability. Its robust new plugin framework

allows everything from image formats, to scripting languages, to

visualization to be extended by the community. The redesigned

data model supports arbitrarily large, N-dimensional datasets,

which are increasingly common in modern image acquisition.

Despite the scope of these changes, backwards compatibility is

maintained such that this new functionality can be seamlessly

integrated with the classic ImageJ interface, allowing users and

developers to migrate to these new methods at their own pace.

CONCLUSIONS: Scientific imaging benefits from open-source

programs that advance new method development and deployment to a

diverse audience. ImageJ has continuously evolved with this idea

in mind; however, new and emerging scientific requirements have

posed corresponding challenges for ImageJ's development. The

described improvements provide a framework engineered for

flexibility, intended to support these requirements as well as

accommodate future needs. Future efforts will focus on

implementing new algorithms in this framework and expanding

collaborations with other popular scientific software suites.",

journal = "BMC Bioinformatics",

volume = 18,

number = 1,

pages = "529",

month = nov,

year = 2017,

keywords = "Extensibility; Image processing; ImageJ; ImageJ2;

Interoperability; N-dimensional; Open development; Open source;

Reproducibility",

language = "en"

}

@ARTICLE{Caicedo2017-ks,

title = "Data-analysis strategies for image-based cell profiling",

author = "Caicedo, Juan C and Cooper, Sam and Heigwer, Florian and Warchal,

Scott and Qiu, Peng and Molnar, Csaba and Vasilevich, Aliaksei S

and Barry, Joseph D and Bansal, Harmanjit Singh and Kraus, Oren

and Wawer, Mathias and Paavolainen, Lassi and Herrmann, Markus D

and Rohban, Mohammad and Hung, Jane and Hennig, Holger and

Concannon, John and Smith, Ian and Clemons, Paul A and Singh,

Shantanu and Rees, Paul and Horvath, Peter and Linington, Roger G

and Carpenter, Anne E",

abstract = "Image-based cell profiling is a high-throughput strategy for the

quantification of phenotypic differences among a variety of cell

populations. It paves the way to studying biological systems on a

large scale by using chemical and genetic perturbations. The

general workflow for this technology involves image acquisition

with high-throughput microscopy systems and subsequent image

processing and analysis. Here, we introduce the steps required to

create high-quality image-based (i.e., morphological) profiles

from a collection of microscopy images. We recommend techniques

that have proven useful in each stage of the data analysis

process, on the basis of the experience of 20 laboratories

worldwide that are refining their image-based cell-profiling

methodologies in pursuit of biological discovery. The recommended

techniques cover alternatives that may suit various biological

goals, experimental designs, and laboratories' preferences.",

journal = "Nat. Methods",

volume = 14,

number = 9,

pages = "849--863",

month = aug,

year = 2017,

language = "en"

}

@MISC{Baker2016-zn,

title = "1,500 scientists lift the lid on reproducibility",

booktitle = "Nature Publishing Group {UK}",

author = "Baker, Monya",

abstract = "Survey sheds light on the `crisis' rocking research.",

month = may,

year = 2016,

howpublished = "\url{http://dx.doi.org/10.1038/533452a}",

note = "Accessed: 2023-3-28",

language = "en"

}

@ARTICLE{Freedman2015-dx,

title = "The Economics of Reproducibility in Preclinical Research",

author = "Freedman, Leonard P and Cockburn, Iain M and Simcoe, Timothy S",

abstract = "Low reproducibility rates within life science research undermine

cumulative knowledge production and contribute to both delays and

costs of therapeutic drug development. An analysis of past

studies indicates that the cumulative (total) prevalence of

irreproducible preclinical research exceeds 50\%, resulting in

approximately US$28,000,000,000 (US$28B)/year spent on

preclinical research that is not reproducible-in the United

States alone. We outline a framework for solutions and a plan for

long-term improvements in reproducibility rates that will help to

accelerate the discovery of life-saving therapies and cures.",

journal = "PLoS Biol.",

volume = 13,

number = 6,

pages = "e1002165",

month = jun,

year = 2015,

language = "en"

}

@ARTICLE{Lambert2019-xl,

title = "{FPbase}: a community-editable fluorescent protein database",

author = "Lambert, Talley J",

journal = "Nat. Methods",

volume = 16,

number = 4,

pages = "277--278",

month = apr,

year = 2019,

language = "en"

}

@ARTICLE{Verdaasdonk2014-js,

title = "Bending the rules: widefield microscopy and the Abbe limit of

resolution",

author = "Verdaasdonk, Jolien S and Stephens, Andrew D and Haase, Julian

and Bloom, Kerry",

abstract = "One of the most fundamental concepts of microscopy is that of

resolution-the ability to clearly distinguish two objects as

separate. Recent advances such as structured illumination

microscopy (SIM) and point localization techniques including

photoactivated localization microscopy (PALM), and stochastic

optical reconstruction microscopy (STORM) strive to overcome the

inherent limits of resolution of the modern light microscope.

These techniques, however, are not always feasible or optimal for

live cell imaging. Thus, in this review, we explore three

techniques for extracting high resolution data from images

acquired on a widefield microscope-deconvolution, model

convolution, and Gaussian fitting. Deconvolution is a powerful

tool for restoring a blurred image using knowledge of the point

spread function (PSF) describing the blurring of light by the

microscope, although care must be taken to ensure accuracy of

subsequent quantitative analysis. The process of model

convolution also requires knowledge of the PSF to blur a

simulated image which can then be compared to the experimentally

acquired data to reach conclusions regarding its geometry and

fluorophore distribution. Gaussian fitting is the basis for point

localization microscopy, and can also be applied to tracking spot

motion over time or measuring spot shape and size. All together,

these three methods serve as powerful tools for high-resolution

imaging using widefield microscopy.",

journal = "J. Cell. Physiol.",

volume = 229,

number = 2,

pages = "132--138",

month = feb,

year = 2014,

language = "en"

}

@ARTICLE{Kolmogorov1933-yn,

title = "Sulla determinazione empirica di una lgge di distribuzione",

author = "Kolmogorov, A N",

journal = "G. Ist. Ital. Attuari.",

volume = 4,

pages = "83--91",

year = 1933

}

@ARTICLE{Swedlow2002-fe,

title = "Live cell imaging using wide-field microscopy and deconvolution",

author = "Swedlow, Jason R and Platani, Melpomeni",

abstract = "The use of fluorescence imaging methods, most recently based on

fluorescent protein technology, and the availability of high

quality fluorescence imaging systems have driven a revolution in

cell and molecular biology. Live cell imaging, especially using

fluorescence, is now used in a wide variety of assays in academic

and commercial laboratories. The use of this technology requires

particular attention to be paid to cell engineering, the design

of the image acquisition system, the imaging protocol, and

subsequent processing and analytic methods. In this review, we

discuss each of these steps, highlighting practical techniques

developed by us and others.",

journal = "Cell Struct. Funct.",

volume = 27,

number = 5,

pages = "335--341",

month = oct,

year = 2002,

language = "en"

}

@ARTICLE{Wilkinson2016-ds,

title = "The {FAIR} Guiding Principles for scientific data management and

stewardship",

author = "Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, I

Jsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak,

Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva

Santos, Luiz Bonino and Bourne, Philip E and Bouwman, Jildau and

Brookes, Anthony J and Clark, Tim and Crosas, Merc{\`e} and

Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo,

Chris T and Finkers, Richard and Gonzalez-Beltran, Alejandra and

Gray, Alasdair J G and Groth, Paul and Goble, Carole and Grethe,

Jeffrey S and Heringa, Jaap and 't Hoen, Peter A C and Hooft, Rob

and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott

J and Martone, Maryann E and Mons, Albert and Packer, Abel L and

Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van

Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and

Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz,

Morris A and Thompson, Mark and van der Lei, Johan and van

Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and

Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and

Mons, Barend",

abstract = "There is an urgent need to improve the infrastructure supporting

the reuse of scholarly data. A diverse set of

stakeholders-representing academia, industry, funding agencies,

and scholarly publishers-have come together to design and jointly

endorse a concise and measureable set of principles that we refer

to as the FAIR Data Principles. The intent is that these may act

as a guideline for those wishing to enhance the reusability of

their data holdings. Distinct from peer initiatives that focus on

the human scholar, the FAIR Principles put specific emphasis on

enhancing the ability of machines to automatically find and use

the data, in addition to supporting its reuse by individuals.

This Comment is the first formal publication of the FAIR

Principles, and includes the rationale behind them, and some

exemplar implementations in the community.",

journal = "Sci Data",

volume = 3,

pages = "160018",

month = mar,

year = 2016,

language = "en"

}

@MISC{Sofroniew2022-nd,

title = "napari: a multi-dimensional image viewer for Python",

author = "Sofroniew, Nicholas and Lambert, Talley and Evans, Kira and

Nunez-Iglesias, Juan and Bokota, Grzegorz and Winston, Philip and

Pe{\~n}a-Castellanos, Gonzalo and Yamauchi, Kevin and Bussonnier,

Matthias and Doncila Pop, Draga and Can Solak, Ahmet and Liu,

Ziyang and Wadhwa, Pam and Burt, Alister and Buckley, Genevieve and

Sweet, Andrew and Migas, Lukasz and Hilsenstein, Volker and Gaifas,

Lorenzo and Bragantini, Jord{\~a}o and Rodr{\'\i}guez-Guerra, Jaime

and Mu{\~n}oz, Hector and Freeman, Jeremy and Boone, Peter and

Lowe, Alan and Gohlke, Christoph and Royer, Loic and Pierr{\'e},

Andrea and Har-Gil, Hagai and McGovern, Abigail",

month = nov,

year = 2022

}

@BOOK{Chakravarti1967-jl,

title = "Handbook of Methods of Applied Statistics: Planning collection of