In cell developer toolbox software

Manufactured by GE Healthcare

Sourced in Belgium

The IN Cell Developer Toolbox software is a core product offered by GE Healthcare. It provides a comprehensive suite of tools for the analysis and quantification of cellular imaging data. The software enables users to efficiently process, analyze, and manage their image-based experiments, supporting a range of high-content screening and cell-based assay applications.

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Lab products found in correlation

Celltracker deep red, by Thermo Fisher Scientific (1 mentions) Inca 2200 imaging system, by GE Healthcare (1 mentions) Oris cell migration assay kit, by Platypus Technologies (1 mentions) Mitomycin c, by Merck Group (1 mentions) Cellmask deep red, by Thermo Fisher Scientific (1 mentions) Triton x, by Merck Group (1 mentions) Flat bottomed 96 well tissue culture plates, by Corning (1 mentions) 4 6 diamidino 2 phenylindole (dapi), by Merck Group (1 mentions) In cell analyzer 1000, by GE Healthcare (1 mentions) Alexa fluor 488, by Thermo Fisher Scientific (1 mentions) Tom20, by Santa Cruz Biotechnology (1 mentions) In cell analyser 2000, by GE Healthcare (1 mentions) Cellrox green, by Thermo Fisher Scientific (1 mentions)

5 protocols using in cell developer toolbox software

Cell Migration Assay Protocols

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Cell migration was evaluated using the Oris™ Cell Migration Assay Kit (PlatyPus Technologies, Oxford, UK) according to the manufacturer’s instructions. In brief, siRNA‐transfected H157 and H413 cells were first treated with 5 μm CellTracker™ Deep Red (Thermo Fisher Scientific) in PBS and incubated at 37 °C for 30 min and then seeded (7.5 × 10⁴ per well) into the wells of the Oris™ 96‐well plate containing Oris™ cell seeding stoppers in quadruplicate. After 24 h, cells were treated with 10 μg·mL⁻¹ Mitomycin C (Sigma) for 3 h before allowing the cells to migrate into the detection zone after removal of the stoppers. Image acquisition of premigration and postmigration were taken with a 4× objective using INCA 2200 Imaging System (GE Healthcare, Chicago, IL, USA). Images were analysed using the in cell developer toolbox Software (GE Healthcare).
Additionally, time‐lapse microscopy was performed in sparse cultures of YAP siRNA‐treated cells as well as the H413 Vect Ct and hDsg3.myc cell lines in 6‐well plate with a 10× objective using INCA 2200 Imaging System at an interval of 20 min for 16–24 h. Videos and manual cell tracking were made with ImageJ and graphs were generated with the ibidi Chemotaxis and Migration tool. The accumulated distance and velocity of random cell migration were analysed in an Excel spreadsheet.

Ahmad U.S., Parkinson E.K, & Wan H. (2022). Desmoglein‐3 induces YAP phosphorylation and inactivation during collective migration of oral carcinoma cells. Molecular Oncology, 16(8), 1625-1649.

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Virus Infection Kinetics Quantification

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Semiconfluent cell monolayers in 96-well plates were inoculated with the viruses indicated above at an MOI of 0.75, which was determined by FFU assays on MDCK cells. After 1 h of adsorption followed by washing with PBS, the cells were overlaid with 1% methylcellulose in modified Eagle’s medium without trypsin, to prevent the release and spread of progeny virus, thereby enabling the observation of foci that resulted from the initial virus infection. After 8 h of incubation at 37°C, the cells were fixed and analyzed by immunofluorescence assays to quantify foci that resulted from the initial virus infection and Hoechst-stained nuclei. Images were captured with an IN Cell analyzer 2000 automated microscope (GE Healthcare). Fields containing both virus antigen-positive cells and cell nuclei were counted by IN Cell Developer Toolbox software (GE Healthcare), as described previously (37 (link)). Infection rates were calculated by dividing the number of infected cells by the total number of nuclei in the same field.

Arai Y., Elgendy E.M., Daidoji T., Ibrahim M.S., Ono T., Sriwilaijaroen N., Suzuki Y., Nakaya T., Matsumoto K, & Watanabe Y. (2020). H9N2 Influenza Virus Infections in Human Cells Require a Balance between Neuraminidase Sialidase Activity and Hemagglutinin Receptor Affinity. Journal of Virology, 94(18), e01210-20.

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Automated Dose-Response Cell Assay

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Cells were plated at 1000 cells per well in flat-bottomed 96-well tissue culture plates (Corning). 24 h later, drugs were added at 4 different concentrations in triplicate technical replicates, with triplicate untreated control wells. 72 h after drug addition, cells were fixed in 4% paraformaldehyde and washed in PBS. For automated microscope analysis, cells were permeabilised with 0.1% Triton-X (Sigma) in PBS, then stained with CellMask deep red (Life Technologies H32721, used at 1:30,000 dilution) and 1 μg/ml DAPI (Sigma) for 1 h. Cells were washed twice with PBS. Cell images were acquired using an InCell 1000 automated microscope (GE), and then analysed using InCell Developer Toolbox software (GE) to determine the number of cells. Data was averaged for the triplicate technical replicates and normalized to the untreated wells. Results from at least three independent biological repeat experiments were entered into Graph-Pad Prism software to determine the dose response curve, IC50 and 95% confidence intervals for the IC50, using the nonlinear regression analysis of log(inhibitor) versus response with a variable slope. Drug details can be found in the supplementary information.

Biddle A., Gammon L., Liang X., Costea D.E, & Mackenzie I.C. (2016). Phenotypic Plasticity Determines Cancer Stem Cell Therapeutic Resistance in Oral Squamous Cell Carcinoma. EBioMedicine, 4, 138-145.

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Mitochondrial Morphology Assay with Citral

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Cells were seeded in 96-well plates at 7.5 × 10³ cells/well in growth media and left overnight in the incubator for the cells to adhere. The following day cells were treated for 24 h with either PBS or 0.1–100 μM citral, in triplicates. Cells were then washed in PBS, fixed in 4% paraformaldehyde for 15 min, washed again in PBS, and left in PBS until staining. The mitochondria were stained with TOM20 (Santa Cruz Biotechnology) and the nucleus with DAPI. Alexa Fluor secondary antibodies were used to stain the mitochondria red (Alexa Fluor 488; Life Technologies). Staining was performed within 7 days of fixing. Image acquisition was performed using an automated imaging platform IN Cell Analyzer 1000 (GE Healthcare Life Sciences) equipped with a Nikon Fluor ELWD 40 × 0.6 objective. Six fields of view were taken from each well in two fluorescence modes (TRITC and DAPI). Raw images were processed and parameters obtained using a customized protocol in the IN Cell Developer toolbox software (GE Healthcare Life Sciences). Cells were segmented using DAPI (cell nuclei) and properties of the mitochondria were obtained. The total area of the mitochondria and the nuclei was assessed. Experiments were performed in triplicates and repeated on at least two separate occasions.

White B., Evison A., Dombi E, & Townley H.E. (2017). Improved delivery of the anticancer agent citral using BSA nanoparticles and polymeric wafers. Nanotechnology, Science and Applications, 10, 163-175.

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Cellular Uptake and ROS Visualization

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Cells were seeded in 24-well plates at appropriate densities (Supplementary Information).
The cells were allowed to settle overnight before being exposed to 7, 14, 35, 70 or 140 nM IONP dispersions for 24 hours. Notably, since the applied NP dispersion volume was adjusted according to the cell density, the NP number/volume cell medium/cell number remained equal in all experiments (Table S1).
After discarding the IONP containing medium, the cells were labelled with CellROX ® green and Rhodamine-2 AM (Molecular Probes, Belgium) to allow visualization of reactive oxygen species (ROS) and free calcium present in the cytosol, respectively. Both were detected using the IN Cell analyser 2000 (GE Healthcare Life Sciences, Belgium) and the acquired data were analysed using in house developed protocols with the IN Cell Developer Toolbox software (GE Healthcare Life Sciences, Belgium). Detailed staining and analysis protocols are provided in the Supplementary Information.

Joris F., Valdepérez D., Pelaz B., Wang T., Doak S.H., Manshian B.B., Soenen S.J., Parak W.J., De Smedt S.C, & Raemdonck K. (2017). Choose your cell model wisely: The in vitro nanoneurotoxicity of differentially coated iron oxide nanoparticles for neural cell labeling. Acta biomaterialia, 55.

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