IMAGE CONTROLS Panel
The IMAGE CONTROLS panel contains controls related to the ScanImage Image Display Figures – MATLAB figure windows which present, in various manners, the most recently acquired image data obtained by ScanImage on each of its up to 4 input Channels. These figures are: the Channel 1-4 displays, Channel 1-4 Max Projection displays, and the Channel Merge display.
Unknown macro: {blue} Levels">Unknown macro: {blue} Levels
These input values, entered directly as numeric values or by using the slider controls, specify the pixel data values of the processed input data for each input Channel that will be mapped to the highest and lowest entries, respectively in the 256-level colormap used to display each Channel's data on the Image Display Figures.
- Pixel data values above the
Unknown macro: {blue}level are mapped to the highest entry in the colormap
- Pixel data values below the
Unknown macro: {blue}levels are mapped to the lowest entry in the colormap
- Pixel data values between the
Unknown macro: {blue}andUnknown macro: {blue}levels are mapped linearly to entries within the colormap.
Refer to Enhanced colormap options and the
dialog documentation for information about the colormap
used for the Image DisplayFigures
The
levels do not affect the data stored to the stored Image Files which remain the original pixel data value without remapping. However the
levels are stored to the Image Header, so it is possible to recover the display used at the time of ScanImage acquisition.
Consider including an excerpt about colormap issues here
Display Rolling Average
: Specifies the number of frames to include in a rolling average computed for the Image Display figures, i.e. to show less-noisy image data.
: Indicates that display rolling average should be locked (slaved) to the
value specifying the number of frames to average for file logging purposes.
Image Display Interactive Tools
This section consists of
that involve graphical user interaction with one of the ScanImage Image Display figures.
The
control selects the target of these and other image interaction tools in ScanImage:
Several features in ScanImage require user graphical interaction – e.g. selection of point, line, or area – with one of the ScanImage Image Display Figures:
and ROI Addition tools (buttons) on the Main Controls panel
- The 4
When any of these graphical interaction tools are selected (button pressed), ScanImage determines which Image Display Figure the user should interact with based on the value specified in the Image Controls. There are 5 valid figures to use with these tools: the Channel <1-4> display figures and the Channel Merge display figure.
By default, is set to None. In this case, the user must first click on the desired Image Display Figure (which must be visible). Following this click, the appropriate interaction for the specific tool (i.e. point, line, or area selection) can be executed. If no figure is clicked within 5 seconds of selecting the graphical interaction tool, then the operation is cancelled.
In cases where the user may want to repeatedly employ the same Image Display Figure when using graphical interaction tools, then the can be specified as one of the 5 valid figures for graphical interaction tools. If a figure is specified, the requirement to first click on the target image display figure is removed.
This button toggles on/off the Matlab zoom tool in the target figure. With the zoom tool, it is possible to zoom in on selected areas of the image, without affecting the scan command signals generated – ScanImage continues to scan the larger scan area determined by the current Configuration.
This is helpful for investigating a subregion of an image without actually scanning a smaller subregion, which often causes excessive photodamage/photobleaching.
This capability is particularly useful for optimizing bidirectional scan configurations at low
levels.
The Matlab zoom tool remains active on the targeted Image Display Figure until the button is pressed again, toggling the feature off. While the feature remains active, the tool's context menu (right-click menu) can be used to zoom back out of regions. Thus the tool allows one to change the selected subregion repeatedly.
This button toggles on/off the Matlab data cursor tool in the target figure. With the data cursor tool, one or more 'datatips' can be added to the target figure, allowing the pixel value at any position in the image to be displayed as a small note. Once added, datatips can be moved freely throughout the image figure, with the noted value updating to reflect the image pixel location.
Show datatip figure here?
The Matlab data cursor tool remains active on the targeted Image Display Figure until the button is pressed again, toggling the feature off. While the feature remains active, the tool's context menu (right-click menu) can be used to add further datatips, as well as to remove datatips. Note that datatips left active when the tool is toggled off will remain displayed – it is often recommended to Delete All Datatips via the context menu before toggling the tool off.
This button will compute and display a Matlab figure containing a histogram of the pixel data values.
- The histogram bins correspond to the 256 colormap entries in the targeted Image Display Figure.
- The histogram counts correspond to the number of pixels assigned to each entry
The computed histogram depends on the
levels selected for the given Channel.
This tool is useful for visually determining the quality the colormap mapping determined by the
levels chosen
This tool cannot be used with the Channel Merge figure
This button will compute and display to the Matlab command line basic statistics (max, min, median, mean, mode) of the pixel data values in the targeted Image Display Figure, as mapped to colormap entries in that target.
The computed statistics depends on the
levels selected for the given Channel.
This tool cannot be used with the Channel Merge figure
Settings Menu
: If checked, the input samples collected for each pixel (see
on the Configuration panel) are averaged, rather than summed, for purposes of both image display and file saving.
Enabling this option makes intensity values for each Image Display window (and hence the
and
levels that are appropriate) independent of the
– and hence independent of the
,
, and
values on the Configuration panel.
No information is lost when averaging samples, since the
, and the
option itself, are stored to the Image File Header. The summed and averaged forms of data display/saving can then readily be computed from the other.
: If selected, two lines crossing the center of each Image Display Window are shown, to allow ready visualization of the image center.
When this option is selected, then
should also be selected in the Configuration panel
PMT Offsets Menu
ScanImage maintains a stored PMT Offset value for each of the input channels, corresponding to the baseline signal level measured on each channel with scanner parked, shutter closed, and the Pockels at minimum transmission. The PMT Offset values are stored to the image file header for each acquisition.
Beginning with ScanImage 3.8, PMT Offset values are per-sample, not per-pixel. Thus the value is not sensitive to the current
indicated in the Configuration panel. The values are sensitive, however, to the
values in the Channels panel.
: Initiates a manual readout of PMT offset value, updating the stored PMT offset value for each of the input channels.
: If selected, the PMT offset values are measured and updated at the start of each acquisition (FOCUS, GRAB, or LOOP).
: If selected, the offset value for Channel N is automatically subtracted from displayed and stored image data for that channel.
Advanced Image Display Settings
These settings can be shown/hidden with the */*/
control at bottom right of main panel
: If selected, the
input samples collected for each pixel are averaged, rather than summed, for purposes of both image display and file saving.
Enabling this option makes intensity values for each Image Display window (and hence the
and
levels that are appropriate) independent of the
– and hence independent of the
,
, and
values.
No information is lost when averaging samples, since the
, and the
option itself, are stored to the Image File Header. The summed and averaged forms of data display/saving can then readily be computed from the other.
: If selected, two lines crossing the center of each Image Display Window are shown, to allow ready visualization of the image center.
When this option is selected, then
should also be selected in the Configuration panel
: A listbox containing several standard options for the Colormap to be used for each of the Image Display Windows. After making a selection, the
button must be pressed for change to take effect.
The selection in the Image Controls panel is just a macro to update the values entered into the
entries in the Channels panel
Users can create their own custom colormap instead, as further described in the Channels panel documentation.
Colormap Options:
- Gray: (Default) An 8-bit grayscale colormap is used for all image display figures
- GrayHighSat: An 8-bit grayscale colormap is used for all image display figures. Pixels with values occupying upper 5% of the range specified by current
Unknown macro: {blue}values (for each channel) are colored red.
- GrayLowSat: An 8-bit grayscale colormap is used for all image display figures. Pixels with values occupying lower 5% of the range specified by current
Unknown macro: {blue}values (for each channel) are colored green.
- GrayBothSat: An 8-bit grayscale colormap is used for all image display figures. Pixels with values occupying upper/lower 5% of the range specified by current
Unknown macro: {blue}values (for each channel) are colored red/green, respectively.
- Jet: The Matlab jet colormap is used with 256 levels (8-bit).
- Red/Green/Gray/Gray: Channels 1 and 2 use monochrome 8-bit red and green colormaps, respectively. Channels 3 & 4 use 8-bit grayscale colormaps.
- Green/Red/Gray/Gray: Channels 1 and 2 use monochrome 8-bit green and red colormaps, respectively. Channels 3 & 4 use 8-bit grayscale colormaps.
: Pressing this button will read the baseline level on each of the PMT input channels. ScanImage stores the most recently measured offset values to the image file header for each acquisition.
The offset values are not applied (subtracted) to the image data displayed and stored to the image file.