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

BMC, Bench Mark Concentration

No original publication (yet), but still: an active link, Nyffeler et al 201?

The BMC program will read data in text format representing experiments linking the concentrations of a substance to the measured results. Typically the survival of cells (in cell culture) is given at various concentrations of a toxicant. The program will not only calculate the IC10 and related values but also evaluate how trustworthy these values are. Output is a number of graphs with the corresponding numeric values.

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

Sambesi, Singular Analysis of Mitochondrial Behaviour and Size

No original publication (yet), so no active link: Krebs et al 201?

Sambesi is a program to analyse the movements of mitochondria in the neurites of neuronal cells. It will take the file generated by a Zeiss microscope as input (.CZI files). Single neurites can be selected and the movement of the corresponding mitochondria will be visualized in a kymograph. The charackteristics of individual mitochondria can be analysed. Results of all numeric data and a full range of pictures are presented in a single Excel sheet.

CaFFEE, Ca Fluorescent Flash Evaluation Engine

Original publication: Hoelting L, Klima S, Karreman C, Grinberg M, Meisig J, Henry M, Rotshteyn T, Rahnenführer J, Blüthgen N, Sachinidis A, Waldmann T and Leist M., 2016, Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants. Stem Cells Transl Med. 5: p476-87.

CaFFEE is a program to evaluate movies generated with the Cellomics automated microscope as input. It will analyse the Ca dependant increase of fluoresence of Fluo-4 labeled cells during time. The program will do this on single cell level. The signals of the cells are followed through time and only cells that "behave" are selected for further analysis. Various filters can be aplied and results are shown in a multi-sheeted Excel workbook.
Will analyse all movies in a sub-directory if so required.

This program will be freely available, complete with handbook and instruction how to install. Unfortunately, the handbook is not finished yet.
If you interested just revisit this website.


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 and download it.

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.