Guide for Using the Stain-iT Cell Staining Simulator

Click the Instrument tab in Stain-iT Cell Staining Simulator.

Knowing your microscope or imaging instrument includes understanding the number of lasers, lamps, light cubes, and filters. Manufacturer web pages typically include information about their models under specifications or features. If you are unable to find your instrument, you can enter the details manually or use the simulated instrument setting. The simulated instrument setting allows you to see all the reagent and dye possibilities.

Custom settings allows you to enter in your specific instrument.

Click the Cell tab in Stain-iT Cell Staining Simulator.

The next step is to select a cell structure or function that you wish to study.

The next step is to enter the fixation status of your sample. The sample preparation directly impacts the reagents and probes used in your experiment. Some reagents are not compatible with fixatives, while others can be used after PFA fixation.

Next, select your desired product type(s). Product types include reagents and secondary antibodies/labeling kits. Multiple reagents can be used to help visualize a given cellular marker. Use the SpectraViewer tool to determine which will provide optimal emitted spectrum.

Excitation light from the instrument is divided into specific spectral channels. When fluorophores are excited by a light source such as a laser or LED, they emit light that can be visualized using distinct filters. Choosing an emission color influences the fluorophore selection associated with the reagent. If you are choosing multiple products, try to spread out the fluorophores to different channels and minimize spectral overlap.

Further filtering by excitation and emission range can help ensure spectral compatibility with your instrument and when using multiple products.

Compatible products based on your selections will populate in the search bar. Choose the reagent(s) of interest and click “add” to visualize the cell staining.

Examine the spectral compatibility of dyes, probes, and reagents with the SpectraViewer tool. The goal is to reduce spectral overlap among the multiple reagents you’ve chosen.

Hovering your mouse or pointer on the SpectraViewer tool will show the wavelength selected and the percentage of excitation and emission of a particular fluorophore associated with the reagent.

Click full screen to get a larger view of the spectrum.

Click on the right corner of the Cell or SpectraViewer to export data and put into your lab notebook.

Click Review and checkout to purchase your selected products.

Confirm quantity and look at the technical specifications of each product. Most products are accompanied by a detailed protocol regarding the use of the product found on the linked product name. Products can be added directly to cart here.