Defining Default Imaging Settings

Select the plate type you are interested in editing. You can add new plate types to the list from ROCK MAKER software.

You can export new plate type definitions by clicking More Actions and selecting Export. The system will save your plate type settings in an .XML file format. You can also use the Import feature to import the file later if needed or if you obtain new plate type settings from FORMULATRIX support.

Select the lightpath of interest. The type of imaging modes available here depends on the imaging types you purchased. The Visible lightpath is the default imaging setting and is always present.

Each lightpath provides slightly different settings for area numbers 3, 4, and 5. If you select Ultraviolet, the Enable For This Plate Type option will show up. Enabling this option allows you to image your experiments using UV lightpath.

This area contains settings for the optics components and resolutions along with the exposure settings to use during plate imaging.

Optics & Exposure Options for Visible Lightpath

Optics & Exposure Options for Ultraviolet Lightpath

• Binning

  Affects image quality and size. Using lower binning values will result in larger resolution and higher-quality images. 1x1 binning provides optimum image quality but requires longer processing time, whereas 2x2 binning provides lower image quality but reduced processing time.

• Gamma

  Affects the contrast of the midtones in the image. Modifying this setting only affects the midtones, without affecting black and white. However, changing this setting affects both the live image and automatic imaging.

• Condenser

  The condenser collects light from the Köhler light source and concentrates it onto the well being examined. Values range from 0 - 100%. At 0%, the iris is fully open, and a cone of light is concentrated at a wide-angle. At 100%, the iris is closed and the light is concentrated in a column of light as opposed to a cone.

  Adjusting the condenser value can improve image contrast. Read Visible Light Imaging for more information.

• Gain

  Used to amplify signal strength in low-light conditions and increase the pixel’s sensitivity to light, in order to make the image brighter.

• Polarizer

  Determines the angle at which the top polarizer lens is projecting the light from 0 - 3600 relative to the bottom stationary polarizer. When the polarizer is set to 900, it will be crossed to the bottom polarizer resulting in a black image, except where there are birefringent crystals making it useful to find protein crystals.

• Exposure Options

  This area determines how exposure settings are used by ROCK IMAGER® during plate imaging. In Visible imaging, you can opt between Fixed Exposure, Auto Exposure From First Drop, or Auto Exposure for Every Drop. For UV imaging, only Fixed Exposure is available.

  • Fixed Exposure: Lets you manually adjust the Brightness and Exposure settings in the corresponding fields. Set the values accordingly so that the image will have enough contrast and not appear too dark.

  • Auto Exposure from First Drop: ROCK IMAGER® will find the optimum exposure and brightness on the first drop on the plate and use those exposure settings for every drop on the plate thereafter.

  • Auto Exposure for Every Drop: ROCK IMAGER® determines the optimum exposure and brightness for each drop before imaging each individual drop on a plate. This is the most common setting.

    Note: The exposure settings for each drop can be different depending on the conditions of each drop.

Drop Location settings determine how ROCK IMAGER® executes the Drop Location algorithm for the selected plate type. Options may vary depending on the imaging methods you purchased.

Drop Location Options for Visible Lightpath

Drop Location Options for Ultraviolet Lightpath

ROCK IMAGER® can execute Drop Location in two ways: Fixed method and Locate Drop method.

• Fixed Method

  Selecting Fixed tells ROCK IMAGER® to use the drop positions defined in the Drop Positions panel when imaging an experiment. If the selected plate type has more than one drop per well, you can instruct the system to image each drop on the well using different zoom settings by selecting the Override Zoom check box.

  

  Override Zoom Option

• Locate Drop Method

  This method instructs ROCK IMAGER® to run the Locate Drop algorithm before capturing images. Before imaging, the system will perform an overview using the zoom value defined in the Zoom box and the objective (for UV lightpath) from the Objective list. The system will find a drop location using these exact settings.

  Note: The Objective and Zoom options are only available if your hardware supports continuous zoom or objective lenses.

  The Missed Zoom option is available when using the Visible lightpath and Locate Drop method. If ROCK IMAGER® fails to locate the drop using the Locate Drop algorithm, the Missed Zoom value will be used to image the drop. The smallest possible value is 1 and the highest is 12.

Locate Drop Method Settings

When using the Locate Drop method, you can further customize how to run the Drop Location algorithm.

Locate Drop Method Settings

From the Method box, you can choose between Standard and Lipidic Cubic Phase (LCP). The LCP method instructs ROCK IMAGER® on how to locate drops on an LCP or glass plate. The other fields determine the optics and camera settings used while the system is locating a drop before imaging.

Advanced Settings Option for Standard Method

• Min. Length (µm): Controls the minimum number of µm in a blob for that blob to count as a drop.

• Max. Length (µm): Controls the maximum number of µm in a blob for that blob to count as a drop.

• White Pixel Min: The minimum range of pixel intensities that maps to white when converting a sobel image to a binary image.

• White Pixel Max: The maximum range of pixel intensities that maps to white when converting a sobel image to a binary image.

• Open Iterations: Determines the number of iterations for the system to run when opening the image in preparation for drop location.

• Max. Aspect Ratio: The maximum ratio between the largest and the smallest Feret diameter of the blob that represents the drop.

Advanced Settings Option for LCP Method

• Min. Drop Size (µm): Determines the minimum size of a drop.

• Max. Drop Size (µm): Determines the maximum size of a drop.

• Drop White Pixel Min: Determines the minimum size of a drop, measured in pixels.

• Drop White Pixel Max: Determines the maximum size of a drop, measured in pixels.

• Drop Open Iterations: Determines how round an object must be to be recognized as a drop.

• LP Open Iterations: Determines how round an object must be to be recognized as a drop.

• LP White Pixel Min: Determines the minimum size of a lipid phase, measured in pixels.

• LP White Pixel Max: Determines the maximum size of a lipid phase, measured in pixels.