Spectrum [TMRE (Tetramethylrhodamine ethyl ester)]

The displayed graphs show the normalized intensity of each compound, with the excitation curve being represented by a hollow dotted line, and the emission curve being a solid line, filled in with the color of the instrument laser used.

To display the information about a specific compound, touch the displayed curve of that compound, and the associated properties will be displayed on the right-hand side of the page. If applicable, a list of similar compounds, as well as related categories, will be displayed as well.

To add one or more spectra to the graph, click either "fluorophore" in the "Add" submenu on the left or click the center of the empty display panel - a menu will appear at the bottom of the page. To view a known dye, scroll down the menu on the left and click to select. The choice currently selected will be highlighted in blue.

To change the current selection, click a different dye name.

To select multiple individual options at the same time, hold the CTRL key while clicking each desired dye.

To select all of a range of dyes, click the first desired choice, hold the SHIFT key while clicking the dye at the end of the desired range.

To search for dyes by feature, use the section on the right and enter in the desired values, then press the ENTER key. The left-side menu will display all dyes with the selected properties. Click one or more choices. (Reminder: hold the SHIFT or CTRL key while clicking to select multiple dyes)

Once all the desired options are highlighted blue, click the yellow "Add to graph" button on the lower right.

To remove a compound, click the "x" to the right of the compound name.

To add one or more excitation sources, click "Excitation Source" in the "Add" submenu on the left part of the screen. A menu will appear below the graph display with common generic lasers displayed on the left. If the desired excitation source is known, click to select. The choice currently selected will be highlighted in blue.

To change the current selection, click a different excitation source title.

If the "Custom" row is selected, a popup box will appear and prompt the user to enter the center wavelength. To exit, click "cancel". To continue, enter the center wavelength value as a number and click "OK". Then repeat the process with the bandwidth number.

The excitation source will now appear on the graph display as a thin vertical line in a color associated with its location on the spectrum.

To search for an appropriate excitation source, use the right-side section to search by part type, manufacturer, or instrument. Once all desired options have been highlighted or selected, click the yellow "Add to graph" button on the lower right side.

To exit out of the menu, click the small "x" on the upper right corner of the gray bar at the top of the menu.

Note: if an excitation source is added to the graph, the rightmost column in the information table at the bottom of the page, (labeled "Peak Intensity" with the excitation source title in parentheses) will show the percentage of the maximum possible intensity for the emission curve of each compound currently on the graph.

To add one or more filters, click "Filter" in the "Add" submenu on the left part of the screen. A menu will appear below the graph display with common generic filters displayed on the left.

To select a known filter, select one or more options on the left menu. If the "Custom" row is selected, a popup box will appear and prompt the user to enter the center wavelength. Enter the value as a number and click "OK". Then enter in the bandwidth number into the new input box and click "OK". The filter will now appear on the display as a semitransparent vertical band in the color associated with its location on the spectrum.

To search for an appropriate filter, use the right-side menu section to search by part type, manufacturer, or instrument. Once all desired options have been highlighted or selected, click the yellow "Add to graph" button on the lower right side. To exit out of the menu, click the small "x" on the upper right corner of the gray bar at the top of the menu.

Note: If a filter is added to the graph, a new column will appear in the information table at the bottom of the page, labeled "Spillover" with the filter shown in parentheses. These percentages are automatically calculated for each compound currently on the graph. A (-) in a table cell represents no applicable spillover.

If a selected compound is no longer of interest, click the checkbox to the right of the compound name as displayed on the bottom of the page to deselect it.

Under the "Display" submenu heading on the left side of the page, the user can choose to "Hide" or "Show" Fill color within the fluorophore emission graph by clicking the words or left side box.

To change the horizontal display axis, click "Set Axis". A popup box will appear on the top of the page with an input box for the starting wavelength. To keep the current number, click "Cancel", or enter the desired starting wavelength into the input box and click "OK". The user will then be prompted to enter an ending wavelength value. Click "Cancel" to keep the current value or enter the desired numerical value into the input box and click "OK". The display will adjust to the desired settings.

If desired, the user may move an excitation source by hovering over the representative vertical line until the cursor changes shape to a symmetrical horizontal arrow; once the cursor has changed shape, left-click and hold while dragging the line to a desired place along the horizontal axis.

To remove a filter from showing on the graph, deselect the check box to the right of the filter title. To remove the filter from the workspace entirely, click the "x" to the right of the filter title.

Click "Show Crosshairs" under the "Analyze" submenu in order to trace the exact curve of the currently-selected compounds" fluorescent intensity across the horizontal axis. This may be a convenient setting for users employing low-contrast screens. Click "Hide Crosshairs" to return to the default.

To predict the response of the fluorophores on the graph to an excitation laser, click "Predict Intensity" under the "Analyze" submenu. A vertical line will appear in the center of the graph display. The user may move this excitation source by hovering over the representative vertical line until the cursor changes shape to a symmetrical horizontal arrow; once the cursor has changed shape, left-click and hold while dragging the line to a desired place along the horizontal axis. The emission graph profiles will change in real time as the line is dragged to various places on the horizontal axis, representing the intensity of response to an excitation source at that wavelength.

Click "Disable Intensity Prediction" to return to the default visual display.

Under the "Export" submenu on the left side of the screen, the user may instantly download the spectrum as a .png file to their computer by clicking "Image" under the "Export" Menu on the left side of the window.

To instead share a link to the graph(s) page, click "Shareable Link" to copy the url to the clipboard. The user may then "paste" the link into an email or other form of digital communication by either using the right mouse button or clicking the "CTRL" and "v" keys simultaneously.