mapper

Overview

The Mapper combines a number of mapping-related functions into one program. It orchestrates the settings and actions of other programs such as the XSG, Ephys, Acquirer, Stimulator, and LoopGUI. It does so based on a parameters specified in the Mapper, and in calibrations programs such as ImagingSys and Photodiode. The pulses to be used for mapping are specified in Ephys, Acquirer, Stimulator. Maps can be analyzed on-line through a helper program called mapperOnlineAnalysisParameters (a built-in userFcn; see below).

File>Open

Use this to specify the directory (e.g. 'mapPatterns') containing the map patterns.

Display

Check/uncheck the entries to see/hide various graphics objects in the mapper figure window, including the current beam location ('Beam'), an array of points representing the stimulus grid ('Pattern'), a circle representing the soma location ('Soma'), and crosshairs through the center ('Crosshair').

Calibrate Pockels

Launches the Pockels cell calibration routine.

Laser Power

Shows the laser power (measured during the last photostimulus) at the back (i.e., back focal plane; BFP) and front (i.e., specimen plane) of the objective. The latter is calculated based on the value of the lens transmission parameter, as entered in the photodiode gui.

ISI

The interstimulus interval used for mapping, in seconds. Needs to match that specified for Ephys, Stimulator, Acquirer, and loopGUI; if not, an error message is shown.

Zero Mirrors

Sets the current beam position to the center of the video camera's field of view (0,0).

Grab Video

Load a video image for mapping.

Beam X,Y

Location of current beam position in micrometers, relative to center of video image (0,0).

Flashing Panel

The controls in the flashing panel enable single or small numbers of flashes to be delivered, in various modes.

Flash #

The number of the next flash to be delivered.

Flash

Launches the (immediate) delivery of a single flash, at the current beam position.

Mouse

Launches the mouse-flash mode of flashing. In this mode, after hitting 'Mouse', the user selects one or more points on the video image using the mouse. For a single site, a single right click is performed at the desired location. For multiple sites, sites are all left clicked until the final site, which is right clicked, terminating site-selection and starting the sequential delivery of flash stimuli. Note that for multi-site mouse-flashing, the interstimulus interval should be set (in the ISI window) and the loopGUI mode (CPU or DAQ) set as desired.

Re-

For re-mouse-flashing. This launches the same flash stimulus/stimuli that were last specified by selecting Mouse and choosing one or more stimulus locations (see above).

 Export Positions

A convenience tool for showing the data for the mouse-selected stimulus location(s). (Not typically used for routine flashing.) 

Soma Panel

A number of functions relating to the soma position(s).

1,2 and X,Y and R

The numbered pushbuttons put the mouse into soma-marking mode in the video image figure. Select a soma location by right-clicking on the soma. The X and Y coordinates of the selected location will be displayed. Tips: after hitting the pushbutton, prior to selecting the site you can still maximize the video image window for more precise soma-marking; also, note that you need to mark something as Ephus will be waiting for a right-clicked input (failure to do so could result in aberrant behavior). R is the distance (in um) between the soma (if two have been selected). Tip: although referred to as 'soma' the features in this panel can be used to mark locations of any sort on the video image window; e.g. an apical dendrite, or the tips of extracellular stimulating/recording electrodes.

Use as Offset

These pushbuttons will apply the X and Y soma position coordinates as the X and Y offsets for the mapping grid (see below). This is typically used to quickly center the mapping grid over the soma, as in the case of excitation profiles.

Mapping Panel

A collection of functions for setting map grid parameters and more.

Map

Launches the map trial. The button text changes to 'Stop' during mapping; however, if you use 'Stop', check that Ephus returns to pre-mapping state correctly. In particular, the file directory system may get corrupted; check that the XSG settings are correct. Best is to let the map acquisition finish on its own.

Map #

The number of the next map to be acquired.

Position #

The number of the next position to be sampled.

dX, dY, deg

These parameters set the map pattern's offsets in X and Y (dX, dY) and the rotation in degrees ('deg'). Consistent with Matlab convention, positive values of degrees give counter-clockwise rotations, negative values give clockwise rotations. The values can be entered in the text boxes, or adjusted with the little sliders with up and down arrows.

Pattern Panel

Stimulus grid parameters. The drop-down menu shows the map patterns available in the currently selected mapPatterns directory.

Spacing

The X and Y spacing can be set independently, or (by selecting the '=' checkbox) set to be equal.

Flip and rotational variants

The checkbox applies a reflection; the drop-down menu applies rotations in multiples of 90 degrees. This allows a total of 8 reflectional/rotational variations on a basic map pattern.

 mapperOnlineAnalysisParameters

Helper program for the Mapper; sets on-line analysis parameters. (File>Open is n/a.) The mode provides options for identifying peaks or averaging. The calculations are done based on analyzing responses over an analysis window (specified in units of samples, from analysisWindowStart to analysisWindowEnd), in comparison with a baseline window (baselineStart to baselineEnd). The spikeThreshold sets the threshold for detection of events (typically but not necessarily spikes). traceNumber specifies the Ephys channel to analyze.