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Using the Plate Type Editor

 

The Plate Type Editor contains settings for all of your plate types. Upon install, the FORMULATRIX support team will configure the properties for optimal image quality and performance. If you need a new plate type added to your imager, then please contact support@formulatrix.com for assistance. We only recommend advanced users to modify these settings. The information below is for lab managers so that they may adjust settings as they see fit.

Note: The screenshot shown below is from a ROCK IMAGER Dual Imager system with SONICC. The options on your screen may vary slightly.

The Plate Type Editor

 

To use the Plate Type Editor:

  1. After you open ROCK IMAGER, click on File and select Plate Type Editor.

  2. Adjust the settings you want to change using the table below as a guide. If you need further assistance, contact FORMULATRIX support.

 
Plate Type

Select the plate you're interested in editing from the Plate Type list. You can add new plate types to the Plate Type list from the ROCK MAKER software (see Adding a Container (Plate Type) in the ROCK MAKER help files). All other fields on the Plate Type Editor are dependent upon the Plate Type selected. Default definitions for each plate type are available by importing a plate definition .XML file (obtainable by support@formulatrix.com), or you can import a previously saved definition file. To import a plate definition file, click the Import from File button, select the desired plate definition (the plate definition should match the actual plate type you would like to use), and click Open. The Plate Type Editor reads the file and applies the information to each field on the Plate Type Editor for the plate type. From there, you can edit the fields on the Plate Type Editor if necessary. X,Y,Z coordinates for the four corner well locations can only be updated if that specific plate type is registered with a barcode and on the imager hand.

For more information on how to set up a plate definition, see Setting up Plate Definitions.

General

The General area includes basic information about the specifications of the plate, including the number of Columns, Rows, and Drops per well and the number of hotel slots required for the plate.

The Drop Position Saving Enabled checkbox determines whether or not the Drop Location Algorithm will run each time this plate type is imaged, or if ROCK IMAGER will save the settings to memory. Imaging time is faster when Drop Position Saving Enabled is selected.

Imaging Arm/Plate Alignment

The Imaging Arm area enables you to choose which imager type you want to use. If you purchased a dual imager system, you will have two Imager options such as Visible and SONICC or Visible and FRAP. You can select the desired imager that you would like to use from the Imager list.

Note: The Imaging Arm options are not available in ROCK IMAGER 2.

The Plate Alignment field contains a file that helps ROCK IMAGER position the plate for imaging. If you want to change the file, click the Vector button, find the file in the Vectors folder, and then click Open.

The Bump on Return option determines whether or not the plate will be bumped on the plate bump before being removed from the imager. When this option is enabled, the plate bump will be used to safely align the plate to ensure that it is positioned correctly in the storage hotel.

If you have a ROCK IMAGER Dual Imager with SONICC or FRAP, you can use the Capture Tuned Drops button to capture images that have been previously tuned for Visible imaging to help you tune the drop locations for SONICC or FRAP imaging. For more information, see Tuning the Drop Locations of a Plate for SONICC or FRAP Imaging.

Note: The Capture Tuned Drops button is only available in ROCK IMAGER 1000 Dual Imager with SONICC or FRAP, and will only enable in Visible imaging mode.

Drop Positions

The coordinates in the Drop Positions field correlate to the corner drops on the plate. From the coordinates of these corner positions, ROCK IMAGER uses linear interpolation to compute the locations of all drops on the plate. You can tune these positions for better images at any time. See Tuning Plates in ROCK IMAGER for more information.

If you have a ROCK IMAGER Dual Imager with SONICC or FRAP, you can use the Calculate from Visible button to use the drop locations for visible imaging as the basis for the drop locations to be used for SONICC or FRAP imaging. See Tuning the Drop Locations of a Plate for SONICC or FRAP Imaging for using the button.

If you have a SONICC imager, check the Apply changes on Visible coordinates to SONICC imager box to apply any drop location changes to both plate definitions (ROCK IMAGER maintains separate plate definitions for dual imagers).

Well Limits

The height limits in millimeters (mm) imposed on the X, Y and Z axes when you are manually inspecting drops. It is recommended to set the Limits to Enabled. When using plates with larger wells (such as Linbro), increase the X and Y values accordingly so that the drop will not appear off center.

Image Mask

Image Masks are related to Auto Scoring, a feature in ROCK IMAGER (requires ROCK MAKER 2.7 or newer). Certain plate types fluoresce, causing false positives. You can "mask" a plate to increase Auto Score accuracy, which will hide the edges of a plate and instruct Rock Image Processor to ignore fluorescence from those areas when computing a positive or negative score for the drop.

Imager Selection Tabs

The number and type of imagers available here depends on the imaging types you purchased. Visible is always present; optional tabs are Ultraviolet, Fluorescence, and SONICC. The fields on the right of the Plate Type Editor depend on the imager tab selected. Each Imager tab also provides advanced options (see below) that can be accessed through the Advanced button.

 

ClosedAdvanced Options on the Visible Imager

The Visible Advanced Tab

Capture Levels

  • Step Size (DoF %) - Determines the amount of depth of field overlap between slices. The default value is 40%, which means that 60% of a slice will be overlapped by the slice next to it. A step size of 100% results in no overlap and the slices are taken at intervals of the defined DoF. To change the default value, type the desired value in the corresponding box.

Note: At the default value of 40%, ROCK IMAGER will produce the highest quality images possible. Increasing the value will reduce image quality, but will also decrease imaging time by decreasing the total number of slices acquired.

Exposure

  • Min Exposure - Determines the minimum exposure value used during plate imaging. To change the Min Exposure value, type the desired value in the corresponding box.

  • Max Exposure - Determines the maximum exposure value used during plate imaging. To change the Max Exposure value, type the desired value in the corresponding box.

Auto Focus

  • Frame Rate - Determines how fast ROCK IMAGER captures slices in a drop during the auto-focus plate imaging.

  • Move Velocity - Determines how fast the imager hand moves along the Z axis during the auto-focus plate imaging.

  • Min Step Size - Limits the number of slices during the auto-focus plate imaging. The default value is 0.04 mm. To change the default value, type the desired value in the corresponding box.

Drop Zoom

  • Override default - Select the Override default box if you would like ROCK IMAGER to use custom drop zooms defined in the Drop #1 and Drop #2 boxes during plate imaging. Using two different drop zooms can be useful for imaging plates that have two different drop sizes.

  • Drop #1 - Type the desired zoom value for Drop #1 in the Drop #1 box.

  • Drop #2 - Type the desired zoom value for Drop #2 in the Drop #2 box.


Override Exposure

Note: This option is only available if you set your Auto Exposure on the Plate Type Editor to Fixed.

  • Override default — Select to enable a fixed exposure for all imaging modes.

  • Objective 1.5 — Type a value to determine the exposure when you are using 1.5x fixed objective.

  • Objective 2.866 — Type a value to determine the exposure when you are using 2.886x fixed objective.

  • Objective 6.24 — Type a value to determine the exposure when you are using 6.24x fixed objective.


For each of these objective settings you can choose values for both Brightness and Exposure.

  • Brightness — Determines the brightness of the light source. The higher the Brightness value, the brighter the light source will be.

  • Exposure — Determines the amount of optical brightness. The higher the Exposure value, the brighter the image will be.

ClosedAdvanced Options on the Ultraviolet Imager

The Ultraviolet Advanced Tab

Capture Levels

  • Step Size (DoF %) - Determines the amount of depth of field overlap between slices. The default value is 40%, which means that 60% of a slice will be overlapped by the slice next to it. A step size of 100% results in no overlap and the slices are taken at intervals of the defined DoF. To change the default value, type the desired value in the corresponding box.

Note: At the default value of 40%, ROCK IMAGER will produce the highest quality images possible. Increasing the value will reduce image quality, but will also decrease imaging time by decreasing the total number of slices acquired.

Exposure

  • Min Exposure - Determines the minimum exposure value used during plate imaging. To change the Min Exposure value, type the desired value in the corresponding box.

  • Max Exposure - Determines the maximum exposure value used during plate imaging. To change the Max Exposure value, type the desired value in the corresponding box.

Auto Focus

  • Min Step Size - Limits the number of slices during the auto-focus plate imaging. The default value is 0.04 mm. To change the default value, type the desired value in the corresponding box.

Drop Zoom

  • Override default - Select the Override default box if you would like ROCK IMAGER to use custom drop zooms defined in the Drop #1 and Drop #2 boxes during plate imaging. Using two different drop zooms can be useful for imaging plates that have two different drop sizes. You can set the following options for both Drop #1 and Drop #2:

    Important: The Objective and Zoom options are only available if your ROCK IMAGER system supports objective lenses, continuous zoom, or digital zoom.

    • Objective - Select the desired objective from the Objective dropdown menu. The available objective options are 2.5, 5.0, and 7.0. ROCK IMAGER will use both zoom and objective settings when locating a drop.

    Note: The objective values available depend on the specifications of your ROCK IMAGER hardware. Please contact support@formulatrix.com if you are interested in upgrading.

    • Zoom - Type the desired zoom value. The minimum value is one and the maximum value is four.

ROI and Drop Location

  • Auto select objective - Select this option if you would like ROCK IMAGER to automatically determine the best objective setting for finding the drop location.

Note: If you select this option, the Fixed objectives option will be disabled.

  • Fixed objective - Select this option if you would like to use a fixed objective for ROCK IMAGER to find the drop location or Region of Interest (ROI). Select the desired objective from the Fixed Objective dropdown menu.

Note: If you select this option, the Auto select objectives option will be disabled.

Override Exposure

Note: This option is only available if you set your Auto Exposure on the Plate Type Editor to Fixed.

  • Override default — Select to enable a fixed exposure for all imaging modes.

  • Objective 2.866 — Type a value to determine the exposure when you are using 2.886x fixed objective.

  • Objective 6.24 — Type a value to determine the exposure when you are using 6.24x fixed objective.


For each of these objective settings you can choose the value for Exposure. Exposure determines the amount of optical brightness. The higher the Exposure value, the brighter the image will be.

ClosedAdvanced Options on the SONICC Imager

The SONICC Advanced Tab

Capture Levels

  • Step Size (DoF %) - Determines the amount of depth of field overlap between slices. The default value is 75%. To change the default value, type the desired value in the corresponding box.

Note: The default value of 75% is utilized to optimize imaging speed. Decreasing the value will increase signal and image quality but will increase imaging time due to acquisition of more slices.

Exposure

  • Min Exposure - Determines the minimum exposure value used during plate imaging. To change the Min Exposure value, type the desired value in the corresponding box.

  • Max Exposure - Determines the maximum exposure value used during plate imaging. To change the Max Exposure value, type the desired value in the corresponding box.

Auto Focus

  • Min Step Size - Limits the number of slices during the auto-focus plate imaging. The default value is 0.04 mm. To change the default value, type the desired value in the corresponding box.

Drop Zoom

  • Override default - Select the Override default box if you would like ROCK IMAGER to use custom drop zooms defined in the Drop #1 and Drop #2 boxes during plate imaging. Using two different drop zooms can be useful for imaging plates that have two different drop sizes. You can set the following options for both Drop #1 and Drop #2:

    Important: The Objective and Zoom options are only available if your ROCK IMAGER system supports objective lenses, continuous zoom, or digital zoom.

    • Objective - Select the desired objective from the Objective dropdown menu. The available objective options are 2.5, 5.0, and 7.0. ROCK IMAGER will use both zoom and objective settings when locating a drop.

    Note: The objective values available depend on the specifications of your ROCK IMAGER hardware. Please contact support@formulatrix.com if you are interested in upgrading.

    • Zoom - Type the desired zoom value. The minimum value is one and the maximum value is four.

ROI and Drop Location

  • Auto select objective - Select this option if you would like ROCK IMAGER to automatically determine the best objective setting for finding the drop location.

Note: If you select this option, the Fixed objectives option will be disabled.

  • Fixed objective - Select this option if you would like to use a fixed objective for ROCK IMAGER to find the drop location or Region of Interest (ROI). Select the desired objective from the Fixed Objective dropdown menu.

Note: If you select this option, the Auto select objectives option will be disabled.

ClosedAdvanced Options on the FRAP Imager

The FRAP Advanced Tab

Capture Levels

  • Step Size (DoF %) - Determines the amount of depth of field overlap between slices. The default value is 40%, which means that 60% of a slice will be overlapped by the slice next to it. A step size of 100% results in no overlap and the slices are taken at intervals of the defined DoF. To change the default value, type the desired value in the corresponding box.

Note: At the default value of 40%, ROCK IMAGER will produce the highest quality images possible. Increasing the value will reduce image quality, but will also decrease imaging time by decreasing the total number of slices acquired.

Exposure

  • Min Exposure - Determines the minimum exposure value used during plate imaging. To change the Min Exposure value, type the desired value in the corresponding box.

  • Max Exposure - Determines the maximum exposure value used during plate imaging. To change the Max Exposure value, type the desired value in the corresponding box.

Auto Focus

  • Frame Rate - Determines how fast ROCK IMAGER captures slices in a drop during the auto-focus plate imaging.

  • Move Velocity - Determines how fast the imager hand moves along the Z axis during the auto-focus plate imaging.

  • Min Step Size - Limits the number of slices during the auto-focus plate imaging. The default value is 0.04 mm. To change the default value, type the desired value in the corresponding box.

Default Optics

The Default Optics field contains the settings for the optics components and resolutions used during drop imaging, including Gamma, Condenser, Gain, and Polarizer.

If you are using FRAP, you will see the Fluoro Light option which enables you to change the fluorescence signal intensity.

If you are using ROCK IMAGER with FORMULATRIX Advanced Contrast Imaging Technology (FACIT), you can control the illumination pattern — such as top-left, top-right, bottom-left, darkfield, and brightfield — to be projected onto a drop through the Illumination list.

If you are using SONICC, you will also see Binning and Sensor.

ClosedBinning

Binning affects image quality and size, with lower binning values correlating with larger, 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.

ClosedSensor

Sensor detects which imaging method is being used in the SONICC imager. The two SONICC imaging methods are Second Harmonic Generation (SHG) or Ultraviolet Two-Photon Excited Fluorescence (UV-TPEF).

ClosedGamma

Gamma affects the contrast of the midtones in the image. When you modify this setting, only the midtones are affected, without affecting black and white.

Note: Changing this setting affects both the live view and automatic imaging.

ClosedCondenser

The Condenser field identifies the current position of the condenser, expressed in the percentage of the condenser's iris that is closed. 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 the 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. The recommended condenser value for drop location is between 70% and 90%. For regular imaging, the recommended value is 0%

ClosedGain

Gain is used to amplify signal strength in low-light conditions and increase the pixels’ sensitivity to light, in order to make the image brighter.

ClosedPolarizer

This field describes the angle at which the top polarizer lens is projecting the light from 0 - 360° relative to the bottom stationary polarizer. When the polarizer is set to 90°, 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.

FACIT illumination pattern

ClosedTop-left

When selected, ROCK IMAGER illuminates the specimen from the top-left corner. The specimen appears bright at the top-left corner, and the rest of the background appears dark.

ClosedTop-right

When selected, ROCK IMAGER illuminates the specimen from the top-right corner. The specimen appears bright at the top-right corner, and the rest of the background appears dark.

ClosedBottom-left

When selected, ROCK IMAGER illuminates the specimen from the bottom-left corner. The specimen appears bright at the bottom-left corner, and the rest of the background appears dark.

ClosedBottom-right

When selected, ROCK IMAGER illuminates the specimen from the bottom-right corner. The specimen appears bright at the bottom-right corner, and the rest of the background appears dark.

ClosedDarkfield

When selected, the specimen appears bright against a black background.

ClosedBrightfield

When selected, the specimen appears dark against a bright background.

Auto Exposure

Auto Exposure settings determine how exposure settings are used by ROCK IMAGER during plate imaging. Selecting Fixed instructs ROCK IMAGER to use the Brightness and Exposure settings in the corresponding fields. Selecting Drop instructs ROCK IMAGER to run the auto exposure algorithm and determine exposure for each drop prior to imaging each individual drop on a plate. This is the most common setting. Selecting Plate instructs ROCK IMAGER to run the Auto Exposure algorithm on the first drop on the plate and use those exposure settings for every drop on the plate thereafter. If the Auto Exposure is set to Fixed, adjust the Brightness and Exposure accordingly so that the image will have enough contrast and not appear too dark.

 

Note: In SONICC imaging mode, you can adjust the exposure by clicking the arrow buttons next to the Exposure box. The exposure value will be rounded to the nearest multiple of 447 ms.

Drop Location

Drop Location settings determine how ROCK IMAGER executes the Drop Location algorithm. Selecting Fixed instructs ROCK IMAGER to use the drop positions defined in the Drop Positions field (area 4). If the plate type you select has two drops per well, you can configure the zoom for both drops 1 and 2 through the Advanced option. Selecting Locate instructs ROCK IMAGER to use the Drop Location algorithm to locate drops. Type the desired Zoom value in the Zoom box and select the desired objective from the Objective list. ROCK IMAGER will use these settings when finding a drop location, with the exact zoom and objectives as defined.

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

The Missed Zoom feature is available only if you are using the Visible camera and the Locate option to define the position of your drop. If ROCK IMAGER fails to locate the drop using the drop location algorithm, the Missed Zoom value will be used to image the drop. The minimum value is one and the maximum value is twelve.

If you are using ROCK IMAGER with FORMULATRIX Advanced Contrast Imaging Technology (FACIT), you can control the illumination pattern — such as top-left, top-right, bottom-left, darkfield, and brightfield — to be projected onto a drop through the Illumination list. If you select Locate, you must also select a method from the Method list. You can select Standard, Fluorescence or Lipid Phase as a method. The available Method options may vary, depending on the imager type you purchased.

 

Standard Drop Locator

Standard Drop Locator settings (available from the Visible tab) instruct ROCK IMAGER how to locate drops before imaging.  You can define Min Length µm, Max Length µm, White Pixel Min, White Pixel Max, Open Iterations, and Max Aspect Ratio.


• 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, which maps to white when converting a sobel image to a binary image.

• White Pixel Max
The maximum range of pixel intensities, which 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.

Note: If the Standard Drop Locator settings appear grayed, select Fixed under the Drop Location.

Fluorescence Drop Locator (FRAP only)

Fluorescence Drop Locator settings (available from the FRAP tab) instruct ROCK IMAGER on how to locate drops while using FRAP imaging. You can define values for Gamma, Polarizer, Exposure, Gain, Condenser, and Brightness. The values that you define for these fields will determine the settings used while ROCK IMAGER is searching for the drop.


• Gamma


Determines the darkness of the light source. The higher the Gamma value, the darker the image will be.


• Polarizer


Determines the polarized color applied to the image. You can type a value between 0 and 360 into this field and see how the color changes on the live image.

• Exposure

Determines the amount of optical brightness. The higher the Exposure value, the brighter the image will be.

• Gain

Determines the amount of digital brightness. The higher the Gain value, the brighter the image will be.


• Condenser


Determines the image’s contrast. The higher the Condenser value, the sharper the contrast will be.

• Brightness

Determine the brightness of the light source. The higher the Brightness value, the brighter the light source will be.

Lipid Phase Drop Locator

Lipid Phase Drop Locator settings instruct ROCK IMAGER on how to locate drops with an LCP or glass plate. You can define the values for Min. Drop Size (um), Drop White Pixel Min, Drop White Pixel Max, Drop Open Iterations, Max. Drop Size (um), LP White Pixel Min, LP White Pixel Max, and LP Drop Iterations.


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

• Drop White Pixel Min		Determine 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. 

• Max. Drop Size (um)		 Determines the maximum size of 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.

• LP Drop Iterations		Determines how round an object must be to be recognized as a lipid phase.
Focus Settings

Focus Level Selection

Think of Focus Level Selection as a capture range. These settings determine how ROCK IMAGER images a drop once it locates one. You can select Auto-focus with Limits, Fixed Range (DoF Limited), or Fixed Range (Interpolated).

• Auto Focus with LimitsIf you select Auto Focus with Limits, ROCK IMAGER runs the Auto Focus algorithm on the drop to pinpoint the best focus level for the drop on the Z axis. Once the focus level is determined, ROCK IMAGER captures images above and below this point, called "slices". The slices are analyzed and compiled by ROCK IMAGER Processor into the Extended Focus Image (EFI) image, which is the default image displayed for the drop in ROCK MAKER. For Auto Focus with Limits, there are four settings which determine how many slices are acquired. The first two settings are Max. focus levels above and Max. focus levels below, which determine the absolute number of slices to be taken above and below the best focus level, respectively. A larger number will result in more slices acquired, whereas a smaller number will result in fewer slices. The other two settings are Focus threshold above and Focus threshold below, which set the focus threshold for slices relative to the best focus level. For example, when the Focus threshold above value is set to .7, all slices that are above the best focus level, and are at least 70% in focus as the best focus level, will be saved. For the focus threshold values, a larger number will result in fewer slices acquired, and a smaller number will result in more slices. ROCK IMAGER takes as many slices as is determined by the more restrictive of these values — max. focus levels or focus threshold. Whichever of these limits is met first by the system will determine the total number of slices acquired.

Auto Focus with Limits is used when the Z position of the drop is inconsistent across the plate. This can be used for hanging drops and LCP plates. It can also be used in SONICC, where you only need to take a small number of slices around the area of focus.

• Fixed Range (DoF Limited)If you select Fixed Range (DoF Limited), ROCK IMAGER will capture slices along the Z axis between the start and stop heights and also determines the best number of slices to take based on the Depth of Field of the optics in use.

The three settings below the Focus level selection determine how the slices are captured. The Start Z and Stop Z values determine the range along the Z axis where ROCK IMAGER captures slices of the drop. The Max focus levels settings equates to how many slices ROCK IMAGER captures before sending the images to ROCK IMAGER Processor.
• Fixed Range (Interpolated)If you select Fixed Range (Interpolated), ROCK IMAGER captures a series of slices along the Z axis between the start and stop values of the Auto Focus range heights. In this case, you set the number of slices ROCK IMAGER takes in the Max focus levels field.

Manual and/or Automatic Auto Focus

The Manual and/or Automatic Auto Focus setting (available from the Visible tab) enables you to limit the movement of Auto Focus. The default values for Auto Focus Range are 0-0.5 mm. To change these values, type the desired values in the corresponding box.

 

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