CytoPacq: a web-interface for simulating multi-dimensional cell imaging

Abstract Motivation Objective assessment of bioimage analysis methods is an essential step towards understanding their robustness and parameter sensitivity, calling for the availability of heterogeneous bioimage datasets accompanied by their reference annotations. Because manual annotations are known to be arduous, highly subjective and barely reproducible, numerous simulators have emerged over past decades, generating synthetic bioimage datasets complemented with inherent reference annotations. However, the installation and configuration of these tools generally constitutes a barrier to their widespread use. Results We present a modern, modular web-interface, CytoPacq, to facilitate the generation of synthetic benchmark datasets relevant for multi-dimensional cell imaging. CytoPacq poses a user-friendly graphical interface with contextual tooltips and currently allows a comfortable access to various cell simulation systems of fluorescence microscopy, which have already been recognized and used by the scientific community, in a straightforward and self-contained form. Availability and implementation CytoPacq is a publicly available online service running at https://cbia.fi.muni.cz/simulator. More information about it as well as examples of generated bioimage datasets are available directly through the web-interface. Supplementary information Supplementary data are available at Bioinformatics online.


Introduction
CytoPacq is a free web-based service for generating synthetic multi-dimensional images of cells and their populations in optical microscopy with accompanying reference annotations. The aim of the service is to provide an easily-accessible graphical interface for generating benchmark datasets suitable for testing and validation of bioimage analysis methods. Based on the difference from an automatically-generated reference annotation, one can easily compare the quality and accuracy of results of bioimage analysis methods, such as segmentation, tracking, or deconvolution.

Trivia:
The web-interface name originates from words "CYTo", "OPTics", and "ACQuisition", where "cyto" originates from Ancient Greek word "kytos", meaning "cell" in english. The connotation of the name itself is "CYTOmetry PACKage".

Important Features
• fully 3D output: specimens are simulated in arbitrary resolution with configurable z-step • time-lapse sequences: ability to generate dynamic sequences with configurable duration of the experiment • phantom fixation: simulations can be reiterated using previously generated digital phantoms 1 • real-life resemblance: employed computational models cover the most common phenomena occurring during real acquisition process • ease of use: easily accessible web-based graphical interface 2 with contextual help, emphasizing the most important parameters • active project: new modules are incorporated as our development on the synthesis of bioimage data advances Note: As the simulation process can take a substantial amount of time, depending on the chosen settings, we do not oblige you to leave the web-interface open in your browser for the whole process. To get back to your simulation later, you can either enter your e-mail (see row marked with an asterisk on Fig. 1) and use the uniquely generated link in the received notification, or you may bookmark the page in your browser. MitoGen module implements a model of HL60 cell population that evolves in time. All the cells are modelled fully in 3D+time. They can move and split due to mitosis that is also simulated. o

Modeling of single cells with filopodial protrusions -FiloGen
FiloGen module realizes a model of single lung cancer cells with evolving filopodia. The cell is modeled fully in 3D+time.

Workflow
The simulation process (see Fig. 2) begins by specifying desired configuration, which you can easily define by filling the input form in the web-interface (see Fig. 1). This configuration is subsequently passed to the appropriate simulator, depending on the chosen type of digital phantom. The simulation output then consists of synthetic images and accompanying reference annotations.

Obtaining the Data
As soon as the simulation is finished, you will be able to obtain the generated data from the download page (see Fig. 3). The download page contains previews of the synthetic images, (selective) downloads of the output data, and links to recommended image viewers. The image previews correspond to each stage of the simulation process, i.e. digital phantom generation, simulation of optical system, and simulation of acquisition device. You are able to download either complete archive, containing synthetic images of all simulation stages with reference annotations in TIFF or ICS format including generated configuration files, or any of mentioned separately. The recommended viewers, Viewer 3D and Viewer 4D, are our in-house developed tools for convenient browsing of 3D images and their sequences, respectively.

Note:
The generated configuration files in INI or JSON format can be used as an input for our simulators, if you wish to install them on your computer and run them offline. More information about particular simulators can be found at: https://cbia.fi.muni.cz/research/simulations-and-modeling.html 5/10

Additional Functionality
The following supplementary services are accessible from the main page.

• Public Benchmark Datasets and their Preconfigured Parameters
Public benchmark datasets, generated by the CytoPacq simulation modules, are available as a part of the Cell Tracking Challenge (CTC, http://celltrackingchallenge.net), Broad Bioimage Benchmark Collection (BBBC, https://data.broadinstitute.org/bbbc), and Masaryk University Cell Image Collection (MUCIC, https://cbia.fi.muni.cz/datasets). Aside from being able to download these public datasets from the main page, user is also offered an option to generate new datasets based on their parameters.

• My CytoPacq, My Benchmark Datasets
My CytoPacq is a personal area, serving as a hub for services facilitating access and manipulation with user data. My Benchmark Datasets is a part of My CytoPacq, allowing user to access data of their previous simulations at any time directly through the web-interface. Furthermore, the data can be used as a basis for another simulation, i.e. user is able to fix a phantom and generate new data using arbitrary configuration of optical system and acquisition device. At the time of writing this text, the phantom fixation is available for microspheres, HL60 nuclei (static and dynamic), granulocyte nucleus, and colon tissue. More services will be added as the development continues. The optional registration is offered to every user who would like to use services in My CytoPacq.

Running the Software on Own Hardware
As described in Section 3, the simulation has three stages, i.e. simulation of digital phantom, simulation of optical system, and simulation of acquisition device. At the time of writing this text, the CytoPacq web-interface utilizes three simulation modules for digital phantom simulation, CytoGen, OptiGen, and FiloGen. The simulation of optical system and acquisition device is implemented in OptiGen and AcquiGen module, respectively.
All simulation modules are freely available in the form of preconfigured virtual machines, containing the simulation modules and corresponding source codes. All virtual machines can be opened in Oracle VirtualBox (https://www.virtualbox.org). More information about running the software on own hardware can be found on the respective web pages of each simulation module. Essential web links are as follows:

Terms of use
The usage of datasets generated by the CytoPacq web-interface (or underlying simulation modules) is endorsed for scientific and educational purposes. The usage for any other purpose (e.g. commercial) is generally possible, but solely with the explicit permission of the authors. All generated data is free of charge and may be used as long as the CytoPacq web-interface is properly acknowledged. More information is available at https://cbia.fi.muni.cz/simulator/terms.php. In case of any questions, please do not hesitate to contact us at cbia-cytopacq@fi.muni.cz. 7/10

List of Available Acquisition Devices
At the time of writing this text, there are 6 available virtual acquisition devices: • CoolSNAP HQ • CoolSNAP HQ2 • iXion DV887 • iXion DU888E