This is the site dedicated to useful software for in vitro toxicology supported by

The Doerenkamp-Zbinden Chair of in-vitro Toxicology and Biomedicine/Alternatives to Animal Experimentation

a.k.a. AG Leist, University of Konstanz

BMCeasy, Bench Mark Concentration

Original publication: Krebs A, Nyffeler J, Karreman C, Schmidt BZ, Kappenberg F, Mellert J, Pallocca G, Pastor M, Rahnenführer J, Leist M. 2020 Determination of benchmark concentrations and their statistical uncertainty for cytotoxicity test data and functional in vitro assays. ALTEX, 37, p. 155-163.

Many toxicological test methods, including assays of cell viability and function, require an evaluation of concentration-response data. This often involves curve fitting, and the resulting mathematical functions are then used to determine the concentration at which a certain deviation from the control value occurs (e.g. a decrease of cell viability by 15%). Such a threshold is called the benchmark response (BMR). For a toxicological test, it is often of interest to determine the concentration of test compound at which a pre-defined BMR of e.g. 10, 25 or 50% is reached. The concentration at which the modelled curve crosses the BMR is called the benchmark concentration (BMC). We present a user-friendly, web-based tool (BMCeasy), designed for operators without programming skills and profound statistical background, to determine BMCs and their confidence intervals. BMCeasy allows simultaneous analysis of viability plus a functional test endpoint, and it yields absolute BMCs with confidence intervals for any BMR. Besides an explanation of the algorithm underlying BMCeasy, this article also gives multiple examples of data outputs. BMCeasy was used within the EU-ToxRisk project for preparing data packages that were submitted to regulatory authorities, demonstrating the real-life applicability of the tool.

This program is running ONLINE, complete with instructions and example file. Just click on the BMC-icon for more information and the link.

Suiker, SUperImposing KEy Regions

Original publication: Karreman, C., Kranaster, P and Leist, M. 2019, SUIKER: quantification of antigens in cell organelles, neurites and cellular sub-structures by imaging. ALTEX, 36, p. 518-520. doi: 10.14573/altex.1906251.

Suiker (program for SUperImposing KEy Regions) quantifies colocalization of different proteins or other features over an entire image field.
Suiker allows the definition of cellular subareas by subtraction ('punching out') of structures identified in one channel from structures in a second channel. This allows e.g. definition of neurites without cell bodies. Moreover, normalization to live or total cell numbers is possible. Providing a detailed manual that contains image analysis examples, we demonstrate how the program uses a combination of colocalization information and fluorescence intensity to quantify carbohydrate-specific stains on neurites. Suiker can import any multichannel histology or cell culture image, builds on user guided threshold setting, batch processes large image stacks and exports all data (including the settings, results and metadata) o be used in Excel.

This program is freely available, complete with handbook and instruction how to install. Just click on the Suiker-icon on the right for the download page.

CaFFEE, Ca Fluorescent Flash Evaluation Engine

Original publication: Karreman, C., Klima, S., Holzer, A.-K. and Leist, M. (2020) “CaFFEE: A program for evaluating time courses of Ca2+ dependent signal changes of complex cells loaded with fluorescent indicator dyes”, ALTEX - Alternatives to animal experimentation, 37(2), pp. 332-336.

Quantification of changes in intracellular free Ca2+ concentrations [Ca2+]i is fundamental to the understanding of the physiology of single cells in response to both environmental and endogenous stimuli. Here we present easy to use freeware that allows especially the evaluation of [Ca2+]i signals in complex and mixed cultures. The program CaFFEE (Calcium Fluorescent Flash Evaluating Engine) enables the user to evaluate the response of hundreds of cells to treat­ments that influence [Ca2+]i. CaFFEE processes large quantities of image data, automatically identifies individual cells in mixed, heterogeneous populations, and evaluates their fluorescence signal. All data are exported in spreadsheet format, and data on thousands of cells can be batch-processed. Moreover, the program optimizes the visual representation of time-lapse image data for user-guided data exploration (setting of parameters for semi-automated data processing). The freeware allows the standardized and transparent processing of imaging data independent of the platform used to gen­erate the data.

This program is freely available, complete with handbook and instructions how to install.
Just click on the CaFFEE-icon on the left for the download page..


Original publication: Nyffeler J., Karreman C., Leisner H., Kim Y.J., Lee G., Waldmann T. and Leist M. (2016), Design of a high-throughput human neural crest cell migration assay to indicate potential developmental toxicants., ALTEX 34, p75-94, doi: 10.14573/altex.1605031.

RingAssay is a program for evaluating the mobility of cells. It will take photos made with the Cellomics automated microscope as input. With this information the program will calculate cell density as a function of distance from the center, number of cells that moved, average distance covered by these cells and it will also do some primitive shape analysis. Output are multicolored pictures in jpg format and all numeric data in an Excel sheet.
Whole 96-well plates are analysed in one run.

This program is freely available, complete with handbook and instruction how to install. Just click on the RingAssay-icon on the right for the download page.

AiO, All in One

Original publication: C. Karreman, AiO, combining DNA/protein programs and oligo-management., 2002, Bioinformatics. 18: p884-885.

AiO (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate and high quality printing with a number of databases. These databases allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment.

This program is freely available, complete with handbook and instruction how to install. Just click on the AiO-icon and go to the download page.