What's New in ROCK IMAGER 3.12?

Version 3.11.4

July 5, 2024

 

Added:

• [SONICC] A feature to select a specific well when analyzing laser power using reference plate imaging.

 

Improved:

• [SPARK Laser] SONICC imaging performance when imaging a plate with SHG and UV-TPEF.

 

Version 3.11.3

January 26, 2024

 

Fixed:

• Mistyping of fluorescence in JSON imaging setting.
• [RMI V4][FRAP] Disabled Auto Exposure field when in Fluorescence (Cy3) imaging mode.
• Mismatch in the imaging setting configuration between ROCK MAKER v4 and ROCK MAKER V3.

 

Version 3.11.2.14

December 15, 2023

 

Improved:

• ROCK IMAGER V3 - ROCK MAKER V4 partial integration using REST API, enabling SetRobot, SetImagingSetting, and SetPlateStateAtImager features while removing data requests from ROCK MAKER V4.

 

Version 3.11.1.1

November 02, 2023

 

Added:

• [RI1000] A feature to enable/disable main door sensor checker for troubleshooting.

 

Version 3.11.0.15

September 19, 2023

 

Improved:

• [Storage Calibration] The “Vector Coordinate” feature to reset the selection when choosing another Hotel.

Added:

• [RI1000] A warning message and a feature to disable plate transfer when the main door sensor is in the open state.
• A feature to remove a specific folder at startup.

Changed:

• [Log] The "FrameErrorcodeExposeDoneNotification" event type to the verbose type (debug).
• The threads’ default config in ROCK IMAGER Processor to two threads and one column.

Fixed:

• [Tools] The software crash when executing "Post-QA Config Reset" for RI1 and RI2.
• [Plate Type Editor] The unautomated Plate Type Info update after changing the Plate Type in ROCK MAKER.
• The unautomated license check before expiration. The license was renewed and the server was updated, but the software didn’t automatically check the license.
• The storage capacity license for RI54.
• [RI1000][Dual Imager] The system failure to execute plate bump sequence when the “OnlyUseHand”, using only one PSR hand, feature was enabled.

Version 3.10 Hotfix 5

September 12, 2023

 

Fixed:

• An issue where the vcredist-checker error message appeared although OpenCV functioned properly.

 

Version 3.10 Hotfix 4

March 1, 2023

 

Improved:

• The system to use MIL for software upgrade without switching to OpenCV Image Processing in case vcredist 8.0 isn’t installed.

 

Added:

• A warning message to replace the automatic laser “clear error” routine and a notification email sent to the support team.
• A feature to inform users when Windows doesn’t use the English (United States) Regional format.
• A warning message when RI fails to load OpenCV.dll.
• A warning message when upgrading the software using OpenCV Image Processing without installing vcredist v8.0.

 

Fixed:

• RI Scheduler failure to execute the scheduled imaging task.
• Overlapping temperature graph resulting from displaying the temperature data from the S1, S10, S11, and S1x sensors in one graph.
• Excessive Schedule Entry Promoter logging.
• Repeated logging of the “Schedule Entry Synchronizer” event when repositioning a plate in the load port.
• [SLP Only] UV exposure error due to different values in“UVOpticsController.config” and in “VisibleOpticsController.config”.
• Deletion of manually added files in the binary folder during the ROCK IMAGER software updates.
• Duplicated schedule in the Future Imaging Schedule queue during an imaging process using the Image Plate feature in the Plates Waiting To Be Imaged menu.
• An issue where the system did not remove the unexecuted imaging schedules for the disabled imager from Plates Waiting To Be Imaged.
• An issue where SONIC’s exposure settings overrides Visible/UV exposure time when RM Imaging Settings is set to 500ms.
• Unclear warning when Rock Imager refuses to perform an imaging task because Rock Maker is set to Disable Imaging.
• Failure to read a shared folder location with curly braces in its location name.
• An issue with the system that only preserved two digits after the decimal point, resulting in the ROI in the ROCK MAKER not functioning properly.
• Software crash when filtering a plate.

 

Version 3.10 Hotfix 3

December 21, 2022

 

Fixed:

• An issue of an unexecuted imaging schedule after ignoring a failed system diagnostic.
• An issue of a darker image due to incorrect exposure value for 1x1 and 2x2 binning when using PointGrey Camera (Grasshopper).

 

Version 3.10 Hotfix 2

August 31, 2022

 

Added:

• (SONICC) A notification to inform users if the ROCK IMAGER Software cannot connect to the LBO Crystal Oven.
• A notification informing users when an error occurs in the SPARK Laser.
• A feature to enable the ROCK IMAGER Processor to automatically restart the ROCK MAKER Server if the ROCK MAKER Server stops running.

 

Improved:

• (RI 182) Software behavior when in the Automatic Mode to return a plate to another empty hotel slot when the previously used hotel slot is filled by another plate.
• Improved software behavior to immediately execute the skipped defrost cycle schedule caused by an unexpected software shutdown. The defrost cycle will be executed right after the software starts.

 

Changed:

• Software behavior to only mail FORMULATRIX Support when the ROCK MAKER ImagerLink encounters an error.

 

Fixed:

• (Single Light Path Imager) An error in the Camera Control panel where the ROCK IMAGER Software displayed unnecessary Brightness field.
• A failed backup process due to an issue with the unsupported file name convention in the Help File attached in the ROCK IMAGER Software.
• An error where the ROCK IMAGER window blocked a dialog box informing users to return the abandoned plate.
• An error where the UV Exposure value from Plate Type Editor was not loaded in the Load Setting box.
• (FRAP) Virtual memory remaining full even after the memory was cleaned.
• (Single Light Path) ROCK IMAGER Software applying the wrong exposure value, causing a darker imaging result.
• An error where the imaging schedule was not deleted even though the plate had been removed from the system.
• An error where the schedule to image a plate immediately was not deleted even though the plate had been removed from the system.

 

Version 3.10 Hotfix 1

June 28, 2022

 

Added: 

• Single Light Path compatibility in the ROCK IMAGER 1000 - Dual Imager (FRAP).
• Software compatibility so now it can run on Windows 11.

 

Version 3.10

May 31, 2022

 

Added:

• (ROCK IMAGER Dual Imager System) Data value in the Current Reading panel of the Temperature Graph window to show the temperature of the additional oven board.
• (SONICC only) A dialog box to inform users if an error occurs in the SPARK Laser during live imaging. A notification email is also sent to the Support team for easier troubleshooting.

 

Improved:

• ROCK IMAGER software behavior to automatically reconnect with the KVaser CAN without the need to restart the ROCK IMAGER software when an error occurs in the KVaser CAN connection.
• Software behavior to automatically turn on the Live Image sub-tab after loading the imaging settings from the ROCK MAKER Software or another LIMS.

 

Fixed:

• An error where the ROCK IMAGER Software commanded to change the objective when the objective was on its way to the default (home) position.
• (Single Light Path) An error where the overexposed state caused Auto Exposure did not produce an optimized result.
• An issue where the ROCK IMAGER Processor could not work when the ROCK IMAGER captured a large number of blank images.
• An error where the ROCK IMAGER software could not run after the software was automatically closed due to a power outage occurred.
• An issue in the Imaging Settings dialog box showing 5 Imaging Settings options listed.
• ROCK IMAGER Processor (RIP) not working properly to process a large number of blank images.
• An issue in the database connection that caused the plate schedule was not updated during Imaging Scheduled Plates mode.
• An issue where the Load Port sub-tab disappeared when the plates with duplicate barcodes were available in the sub-tab.
• (SONICC only) A software crash that happened after a power cycling on the SPARK Laser hardware then followed by turning on the laser via the ROCK IMAGER Software.

ROCK IMAGER 3.9 provides you both software and hardware improvements for all types of imagers and optical setups to make your research easier, including a new camera driver and barcode scanner compatibility. You can read the full details in the release notes below.

All ROCK IMAGERs

• Revamped Temperature Graph
  
  The Temperature Monitor in ROCK IMAGER, now called the Temperature Graph, includes several improvements that make it easier to use. Hover over the temperature sensor list to highlight the corresponding data line on the graph. You can also scroll the mouse wheel to slide the graph to the left or right to easily see how the temperature data has changed over time, or scroll the mouse wheel while pressing the Ctrl key to zoom in and out of the graph. To find out more about the changes made to the Temperature Graph, read Viewing the Temperature Graph.

The Temperature Graph in ROCK IMAGER 3.7

 

• Optimized the Visible Extended Focus Image (EFI) View for Better Crystal Detection
  
  The image processing library performance has been optimized in ROCK IMAGER 3.7 to improve the image quality of EFI for Visible imaging. This helps you catch crystals that were previously undetected.

EFI View Prior to Optimization (Left) and EFI View After Optimization (Right)

 

• Load Imaging Settings from ROCK MAKER in ROCK IMAGER Manual Mode
  
  In Manual Mode, you can now select any of the imaging settings defined in ROCK MAKER to view the live image. When opening the live image the new Load Setting window will appear, allowing you to easily see how the image changes as you switch between imaging settings. For more information, see Manually Inspecting Plates.

Selecting an Imaging Setting for the Live Image in Manual Mode

 

ROCK IMAGER 2

• Ability to Select Slots When Imaging a Plate
  
  If you have two plates on the imager hand, the latest ROCK IMAGER software allows you to image a single plate without having to eject the other one. Choose one or both plates to be imaged by selecting the checkboxes of the Select Slots option in the Image Plate Using window. This option is available when using either Image Plate or Image Plate Using in the Image option of the Imager menu. See Imaging a Plate with RI 2 for more information.

Select Slots Option as Seen in the Image Plate Using Window

 

• Added a Check for Plate Type Prior to Imaging
  
  ROCK IMAGER 3.7 can automatically check the plates on the imager hand and let you know to remove one of the plates if they are of different types, as imaging two different plate types at the same time could cause a collision. The warning message, as shown in the below image, will appear when you select either Scan Plate(s) from the Imager menu, or Load Plate Type from the Plate Control panel in the Imager tab.

New Warning Message in ROCK IMAGER 3.7

 

Multi-Fluorescence Imaging (MFI)

• Auto Exposure Enabled for Visible Fluorescence Imaging
  
  Auto Exposure is now enabled for Visible Fluorescence imaging on MFI imagers. With Auto Exposure, ROCK IMAGER can optimize the exposure and brightness settings on a per drop or per plate basis, giving you high contrast images without oversaturation. During a manual imaging session, use the Auto button in Camera Control panel to run the auto exposure algorithm. While in automatic imaging, you can define the Auto Exposure settings from the Plate Type Editor. This way you get better images without having to worry about optimizing your imaging settings manually. See Imaging Plates with MFI for more information.

Using the Auto Exposure Button While Performing Live Imaging (Left) and Defining the Auto Exposure Settings for Automatic Imaging (Right)

 

Minor Software Changes

ROCK IMAGER has added several minor changes for better usability. Other changes include:

• ROCK IMAGER 3.7 includes some improvements to the Plates tab. Each plate’s status will now be marked with different text colors for easier identification. You can also hover the mouse pointer over the plate list to quickly view a brief description of that plate. See Plates Tab for more information.

The Plate Status in the Plates Tab

 

• A warning message will now appear when upgrading the ROCK IMAGER PROCESSOR (RIP) to the latest version when the ROCK IMAGER software hasn’t been upgraded yet. This message reminds you to upgrade the ROCK IMAGER software after upgrading the RIP, to prevent any compatibility issues.

Reminder to Upgrade the ROCK IMAGER Software after Upgrading RIP

 

• ROCK IMAGER now detects if one of your imagers has been updated to a newer software version. To prevent any compatibility issues, a notification message appears to recommend you to also upgrade the ROCK IMAGER installation that you are currently using.

ROCK IMAGER Upgrade Notification

All ROCK IMAGERs

• Windows XP Is No Longer Supported
  ROCK IMAGER 3.6 only supports Windows 7 (32-bit or 64-bit) and Windows 10 (64 bit). Please contact support@formulatrix.com if you need help upgrading your Windows operating system.

Warning Message for Windows XP Users Upgrading ROCK IMAGER to Version 3.6

 

Important: If you are using Windows XP, you cannot upgrade beyond ROCK IMAGER version 3.5 unless you upgrade your Windows operating system to a supported version.

 

ROCK IMAGER 1000 Dual Imagers

• Quickly and Easily Calibrate a New Plate with the Improved Plate Type Editor
  You can easily calibrate plates for SONICC or FRAP imaging with the new Calculate from Visible button in the Plate Type Editor. This button enables you to automatically generate the drop coordinates, which have been previously tuned for visible light imaging, to calibrate your new plate for SONICC or FRAP imaging. The Calculate from Visible button is only available for ROCK IMAGER Dual Imager with SONICC or FRAP integration. To learn how to tune drop locations in ROCK IMAGER, see Tuning Plates in ROCK IMAGER.
  

Calculate from Visible Button

 

SONICC

• Laser Status Is Now Displayed in the Status Bar
  SONICC users can now easily see whether the SONICC laser is powered on or off from the Status Bar in the ROCK IMAGER software. This feature applies to both SONICC Benchtop and ROCK IMAGER Dual Imager with SONICC integration.

Laser Status as Shown in the Status Bar

 

Minor Software Changes

ROCK IMAGER has added several minor changes for better usability. Other changes include:

• ROCK IMAGER 3.6 includes several improvements to the Application Programming Interface (API) for users of RI 1000 with Automation Port Integration. New API commands have been added to help you easily manage your instrument and retrieve the status of different ROCK IMAGER components. The API now also supports the Representational State Transfer (REST) protocol, which supports .JSON data format. Please contact support@formulatrix.com for more information about API.

 

• Improved the EFI behavior when performing manual imaging to automatically turn off the Live Image mode and all illumination sources, including UV, brightfield, and the SONICC laser, after completing the EFI capture. This feature will prevent any damage being caused to your samples by unintentional and undesired exposure.

 

• The Applied Exposure value visible in the Camera Control panel now shows you the exact exposure value applied to your images. Previously the Applied Exposure value was rounded up to the nearest integer, but now the exact value is shown to two decimal places. This value is calculated by dividing the selected Exposure value by the selected Binning value.

 

The Applied Exposure Value in the Camera Control Panel

SONICC

• Support for the new and improved Photo Multiplier Tube (PMT) for better SHG Imaging. The new SONICC hardware features an improved Photo Multiplier Tube (PMT), which dramatically increases image quality for SHG imaging. This new PMT achieves a 5x improvement in sensitivity allowing you to see crystals you could not see before. Users with a SONICC instrument purchased prior to January 2018 can contact sales@formulatrix.com for a quote to upgrade their PMT.

 

       

 Image Obtained Using the Old PMT                                                                                   Image Obtained Using the New PMT

 

Minor Software Change

• For users with the new PMT installed, ROCK IMAGER now includes the LBO Crystal Oven status in the Status Bar for you to easily see the current temperature of your LBO crystal oven.

 

Crystal Oven Temperature as Shown in the Status Bar

All ROCK IMAGERs

• ROCK IMAGER is now Windows 10 compatible. ROCK IMAGER now supports Windows 10 (64-bit). However, due to the lack of a suitable QImaging camera driver, certain customers may need to purchase a new camera for their imagers in order to use future versions of ROCK IMAGER software on Windows 10 (64-bit). Please contact sales@formulatrix.com for a quote or support@formulatrix.com to determine whether or not your camera needs to be replaced, if you intend to upgrade to Windows 10.

Important: ROCK IMAGER version 3.5 is the last version that will support Windows XP. For future releases of the ROCK IMAGER software, the RI server will need to be upgraded to a supported version of Windows: either Windows 7 (32-bit or 64-bit), or Windows 10 64-bit. Please contact support@formulatrix.com if you need help upgrading your Windows operating system.

• ROCK IMAGER Memory Optimization. The previous ROCK IMAGER release (version 3.4) had some severe problems with memory leaks, which affected some of our customers. A few heavy ROCK IMAGER users reported frequent crashes and the need to restart ROCK IMAGER once a day. With ROCK IMAGER 3.5, memory use has been optimized to stop these crashes from happening. Lower memory consumption also improves the performance of ROCK IMAGER and your PC as a whole.

• Auto-Leveling Enabled for Extended Focus Image (EFI) View. The latest ROCK IMAGER software enables you to use the auto-leveling feature when you are in Extended Focus Image (EFI) view. This feature allows you to more clearly view crystals from the ROCK IMAGER software. For more information, read Extended Focus Image (EFI) Sub-Tab.

 

EFI View Prior to Auto-Leveling	EFI View After Auto-Leveling

 

• Use Digital Zoom on Drop Locations and Regions of Interest for UV and MFI Imaging. ROCK IMAGER 3.5 enables you to use digital zoom for Ultraviolet (UV) and Multi Fluorescence Imaging (MFI) imaging. This zooms in your UV and MFI images to the same field of view (FOV) as visible images, so that when you view them in ROCK MAKER you don’t need to zoom in manually. To enable digital zoom, change the Drop Location from Fixed to Locate in the Plate Type Editor. For more information, read Using the Plate Type Editor. Please note that this feature will work only if you have a 9 MP UV camera. Contact support@formulatrix.com if you need help finding your camera type.

 

ROCK IMAGER 1000

• Stop the Ejection of Expired Plates. ROCK IMAGER 3.5 provides you with the Cancel Eject Expired Plates option in the Load Port menu to stop the movement of all expired plates from the hotel storage to the load port. This way, you will be able to easily add new plates to the load port without having to wait for the expired plates’ ejection process to finish.

Cancel Eject Expired Plates 

All ROCK IMAGERs

• Auto Exposure Enabled for Visible Fluorescence. Auto Exposure is now enabled for Visible Fluorescence imaging on MFI imagers. With Auto Exposure, ROCK IMAGER can optimize the exposure and brightness settings on a per drop or per plate basis, giving you high contrast images without oversaturation. This way you get better images without having to worry about optimizing your imaging settings manually.

Auto Exposure Settings for Visible Fluorescence

 

• Synchronized ROCK IMAGER User Group Quotas. The latest ROCK IMAGER has been optimized to automatically update the group quota information from ROCK MAKER, ensuring that each group member has access to the correct number of plates. ROCK IMAGER can update the plate quota information without restarting the software, allowing you to work uninterrupted. If your plate quota has almost been met, each member of your group will receive an email notification so that you can make any necessary adjustments.

 

• Camera Driver Optimized for Faster UV and Multi-Fluorescence Imaging (MFI). The camera driver has been optimized for UV imaging and MFI, to give you the fastest results possible. This new optimization reduces imaging times for all captures with exposure times greater than 30 milliseconds, making it ideal for UV imaging and MFI.

 

• ROCK IMAGER Maintenance Email Notification. Now the ROCK IMAGER Administrator will receive an email notification 14 days before your ROCK IMAGER maintenance agreement is set to expire. This way you can have more time to extend your maintenance contract, so that you can keep your ROCK IMAGER software up to date and enjoy all of the latest features. Please note that FORMULATRIX software comes with a perpetual license that you own for life. Maintenance is not required to continue its use. For more information, read License Activation and Reactivation.

ROCK IMAGER Licensing Email Notification

 

ROCK IMAGER 1000

• Access Even More LCP Plates. Now ROCK IMAGER enables you to scan all plate slots when using the LCP imager, including the rows at the top hotel, unreachable until now. With this feature, you can maximize the LCP plate imaging to all available plate rows, especially when all other slots are occupied. Please contact support@formulatrix.com to enable this feature.

 

SONICC

• Improved SONICC Exposure Field. The ROCK IMAGER UI has been improved to display the actual exposure time for SONICC imaging, along with arrow buttons for easy adjustment. This way you can quickly change the exposure time for your SONICC experiments. All exposure times will be rounded to the nearest multiple of the SONICC frame time of 447 milliseconds. For more information, read Best Practices.

Improved SONICC Exposure Field with Added Narrow Buttons

 

• Display all Imaging Modes in ROCK IMAGER Scheduler. ROCK IMAGER scheduler now lists all types of imaging to be used for scheduled imaging sessions, such as UV-TPEF or SHG. This makes it easier to see what projects are being imaged at a glance.

Complete Imaging Mode Information in ROCK IMAGER Scheduler

 

Minor Software Changes

ROCK IMAGER has added several minor changes for better usability. Other changes include:

• Added a notification when a user tries to move the reference plate to the load port. The reference plate can only be moved by administrators or FORMULATRIX support, for troubleshooting purposes.

• Added a SONICC laser warning notification to inform the user when the laser is turned off.

• Added larger dialog boxes to the ROCK IMAGER Tools panel to make it easier to find what you are looking for.

• Added more information to the ROCK IMAGER Processor log file to make it easier to distinguish between multiple ROCK IMAGER systems.

• The ‘Lost ROCK MAKER Database Connection’ notification will display until the connection is regained. A notification panel also appears in the ROCK IMAGER status bar.

• Changed ROCK IMAGER scheduler so that the “*” schedule priority value can now be edited.

   

All ROCK IMAGERs

• Optimized Condenser Imaging
  Just as polarized imaging has been improved in the previous version of ROCK IMAGER, ROCK IMAGER 3.3 now also optimizes condenser imaging for a faster imaging process and more accurate results. With this new optimization, condenser imaging will be completed first across the entire plate, rather than ROCK IMAGER switching between imaging modes for each well.
  
  

• Revamped Temperature Monitor
  The Temperature Monitor’s interface has been significantly improved, allowing you to analyze your system’s temperature at a glance. Now you can display all of the available temperature data from any given range of time. For easy data comparison, you can select multiple sensors to be displayed at the same time. You can also use the mouse wheel to zoom in and out of the temperature graph to view different data intervals, such as hours, minutes, or even seconds. For more information, please read Viewing Temperature Graphs.

Temperature Monitor

• Better Imaging Results with Fixed Exposure on Single Light Path (SLP) Systems
  Fixed exposure can now be set individually for each objective on SLP systems, providing you with better image quality than ever before. This is particularly useful for drop location where the different objectives are used from drop to drop. You can find this new feature in the Plate Type Editor on the Advanced Tab under Fixed Exposure. Check the Override Default box to edit. If you have any questions on how to optimize your exposure times, FORMULATRIX support is always available to help. For more information, please read Using the Plate Type Editor.

Override Exposure Option in the Visible and UV Advanced Tab of the Plate Type Editor

• Improved Imager Event Log
  Save time by specifying the time frame of interest in the ROCK IMAGER event log to show only the data that you are looking for.

ROCK IMAGER 182 and 54

• Automatically Locate Empty Slots with Smart Imager Hands
  Now ROCK IMAGER 182 and 54 systems will automatically find an empty storage slot for a plate, should that plate’s usual slot be full. If you add a new plate in ROCK IMAGER to a slot that had been occupied by a plate on the imager hand, the imager will automatically find a new slot for the plate being imaged when imaging is complete. If all slots are currently occupied, you will receive a notification in the ROCK IMAGER software, so that you can reorganize your plates.

SONICC

• New Alert Notification for Laser Power
  Rock Imager 3.3 now sends you and our support team an email notification should the laser power increase by more than 100%. Large fluctuations in laser power may indicate that there is a problem with your SONICC system. This notification allows support to quickly investigate any potential issues, while minimizing the disruption to your work.

All ROCK IMAGERs

• Digital Zoom for 9 Megapixel Cameras
  Now all ROCK IMAGERs with nine megapixel cameras, including new systems, have the ability to use digital zoom with fixed objectives. This enables you to tighten the field of view perfectly to the edges of your drops. The digital zoom is achieved by cropping the images acquired by the camera. For more information, see Using Optics Control.

  

• Capture Extended Focus Images (EFI) with a Single Click
  Rock Imager's EFI functionality now includes the ability to view and save extended focus images within ROCK IMAGER. Just click the EFI button on the Camera Control panel to see and save your images, without having to switch to ROCK MAKER. For more information, see Extended Focus Image (EFI) Sub-Tab.

  

  An EFI Displayed on the EFI Sub-tab

• Optimized Polarized Imaging
  Rock Imager 3.1 features polarized imaging optimization to speed up the imaging process and preserve accurate exposure for better images. Using the new optimization, whole plates will be imaged using the selected imaging modes, rather than ROCK IMAGER switching between imaging modes for each well.
  

• Dynamic Image Scheduling
  Plates will now be sent to the imaging queue 4 hours before their scheduled imaging time to reduce wait times between imaging sessions. This occurs only when ROCK IMAGER is idle, so affected plates will be imaged directly if there is no other imaging session currently taking place. For more information, see Scheduling Tab.

• View the Applied Exposure on Live Images
  Rock Imager now displays the applied exposure value for live images on the Camera Control panel. This shows you the exposure value as adjusted by binning exposure compensation. By default, binning exposure compensation is enabled for all visible light images and disabled for all UV images for both PointGrey and PixeLINK cameras. To read more about binning, see Using Camera Controls.

  

  The Applied Exposure on the Camera Control Panel

 

ROCK IMAGER 1000

• Eject Expired Plates Automatically
  Rock Imager makes it even easier to manage plates in storage with the ability to automatically move expired plates to the load port. You will be notified via email when plates are moved so you can keep track of where plates are located. This feature can be enabled from the Load Port menu in ROCK IMAGER and is configured to run from 9:00 to 17:00 Monday through Friday. To change the time settings, please contact support.

 

SONICC

• Image in Visible Light even with SONICC Non-operational
  Now visible imaging schedules will be imaged even while the SONICC laser is non-operational. All SONICC imaging sessions will stay in the imaging schedule and will run automatically after SONICC has resumed functionality.
  
  

FRAP

• FRAP data is retained even when focus level saving is disabled
  You can now disable saving individual focus level images and still retain all the associated FRAP information. All associated FRAP images, such as pre-bleach, end-state and charts, will be saved regardless of database management and whether or not visible or UV focus level images are saved.

• Validation added to ensure accurate FRAP results
  When analyzing a plate with High Throughput FRAP, ROCK IMAGER uses a software algorithm to align the pre-bleach and end-state images. If the algorithm fails to align the images within the specified offset tolerance, no FRAP results are calculated. Instead, an image with an error message is displayed in ROCK MAKER and a score of “-1” is given, alerting you to the FRAP analysis failure. For more information, see Interpreting FRAP Offset Information.

HT-FRAP Images on ROCK MAKER

 

ROCK IMAGER 1000 and 182

• Move multiple plates to the load port
  Managing plates is easier now that ROCK IMAGER enables you to move any number of plates to the load port at once, saving you time. If the load port is currently full, the plates will remain queued and automatically be moved as space becomes available. For more information, see Removing Plates.

 

Multi-Fluorescence Imaging

• Adjust the Field of View (FOV) with continuous zoom imaging
  In addition to the multiple objectives available, ROCK IMAGER MFI allows for continuous zoom imaging. This control enables you to tighten the FOV perfectly to the edges of your drops and is achieved by cropping the images acquired by the camera. The FOV for fluorescent images will match the FOV for visible images for comparison purposes. For more information, see Using Optics Control.

  

  Fluorescence Optics Controls

 

All ROCK IMAGERs

• Optimized plate handling
  With optimized plate handling, ROCK IMAGER will no longer acquire drop overview images for drop locations that have previously been defined in ROCK MAKER. This is especially useful for double imagers, allowing plates to be imaged immediately in SONICC without first having to go to the visible imager to acquire an overview image.

 

Other ways ROCK IMAGER 3.0 can make life easier:

• The display for resolution and image size have been split up and renamed as “Binning” and “Image Size” to accurately display the size of the image in pixels. For MFI images, the image size will be affected by the zoom control and image cropping on the camera.

• Labels for the temperature sensor were changed from "Mid Back" and "Top R" to “Middle” and “Top”.

ROCK IMAGER 2.17 supports two new imaging types: Multi-Fluorescence Imaging and UV absorption Imaging. ROCK IMAGER 2.17 is a limited release for RI-1000s and RI-2s that include either of these imaging types.

• Multi-Fluorescence Imaging (MFI)
  MFI is a new hardware module that is optional for ROCK IMAGER 1000 or ROCK IMAGER 2 models. MFI has three different filter modules that allow you to capture the intrinsic UV fluorescence from aromatic amino acids or to detect fluorescence from labeled proteins. MFI is especially useful in differentiating between crystals of a protein-protein complex and crystals of just one protein. For more information, see Multi-Fluorescence Imaging (Optional).

MFI Sample Images - Visible, Texas Red, Ultraviolet, and Fluorescein (Cyan)

 

• Ultraviolet (UV) Absorption Imaging
  UV absorption is a new hardware setup that allows scientists to acquire absorption images. The UV absorption imager transmits UV light through the sample and then detects the same wavelength UV light on the camera. Areas that absorb the UV light create contrast, allowing you to see differentiating features in your crystallization drops. UV absorption can be helpful for imaging drops that are not UV fluorescence, for example, DNA, RNA, and proteins without tryptophan. For more information, see UV Absorption Imaging .

   

  UV Absorption Imaging Samples

ALL IMAGERS

• Improved Drop Location
  Rock Imager’s drop location algorithm has been improved to differentiate droplet condensation, LCP plate tape, and semi-circular objects from sample drops.

Before Improvement

After Improvement

 

• Better handling of troubled plates
  “Troubled” plates, or plates that were not able to be imaged due to barcode label issues and/or plate alignment issues, are now listed in the Plates Waiting To Be Imaged and Future Imaging Schedule tables in red text. These plates will be skipped and not imaged as scheduled until the problem is resolved. Contact FORMULATRIX support if you need assistance handling troubled plates. For more information, see Scheduling Tab.

Troubled Plates Marked in Red Text

SONICC

• More accessible SONICC reference plate data
  A new SONICC reference plate data analysis menu provides the ability to both view and export reference plate data analysis directly from ROCK IMAGER and execute the reference plate image and analysis routine with a quick click of a button. To take advantage of this feature, benchtop users must contact support to properly create initial readings that will be used as a benchmark for comparison purposes during subsequent imaging and analysis. For more information, please see SONICC Reference Plate Image Analysis.

 

FRAP

• Improved FRAP diffusion rate calculations
  FRAP Full Recovery diffusion rate calculations are now more accurate due to constraining the image alignment algorithm. A calculated image overlay deviation greater than 10 pixels (~ 12 µm) are assumed to be inaccurate and a (0 µm, 0 µm) delta data point is used instead.

  Before Improvement -- Notice Invalid Data Point Affecting Curve Graph (Circled in Red)	After Improvement

 

• Additional FRAP imaging data available in ROCK MAKER
  Two new FRAP imaging parameters, “End-State image offsets” and “Post-Bleach image offsets” are now available on ROCK MAKER’s Imaging Settings tab for high-throughput FRAP imaging sessions. If the difference in the measurements of the Post-Bleach and the End-State image offset values is too great, the imager may be experiencing abnormal plate movement during imaging which could cause invalid mobile fraction and recovery curve data. For more information, see Interpreting FRAP Offset Information.

Offset Values in ROCK MAKER

ALL IMAGERS

• Enhanced automatic drop location
  The automatic drop location detection algorithm has been enhanced to identify the larger circular “blobs” instead of smaller subsections of the drop that previously resulted in false positives. The image below shows the blue box that had previously been used as the drop location and now the red box correctly locating the protein drop. False positives from condensation droplets have also been reduced by changing the maximum aspect ratio to 1.5.

Enhanced Automatic Drop Location

• Improved Auto-Exposure
  The auto-exposure algorithm has been modified to provide better images when executing the Auto-Exposure command. The code has also been adjusted to support different settings for the various cameras we have installed in the field.
  
  

• Image Now imaging priority read from Rock Maker
  The automated imaging schedule now stays properly prioritized despite on-demand imaging requests from ROCK MAKER users, as ROCK IMAGER now reads imaging priority from ROCK MAKER “image now” commands, including image plate now, image drop now, and image plates now (multi-plate experiments). Requires ROCK MAKER 3.2.4.5 or newer.

  

• New online help file
  The help file is now hosted online so that you have immediate access to the most up-to-date information. If your imager does not have internet access, ROCK IMAGER will load a local version of the same file which will load in a web browser.

 

• Plate location information sent to Rock Maker
  Rock Imager now sends additional information about plate location to ROCK MAKER. In the future, ROCK MAKER will show customers if a plate is not in an imager, and provide information about which imager a plate is located in if a customer has multiple systems. ROCK MAKER will also disable all “Image Now” commands if a plate is not inside an imager.

UV

• Rounded UV zoom values
  Zoom values for UV imaging are now rounded to the tenths decimal place.

 

 

SONICC

• Automatic SONICC laser health monitoring
  SONICC reference plate images are now analyzed to monitor the health of the SONICC laser. If image degradation is detected, ROCK IMAGER sends an email alert. Relevant information has also been added to the nightly diagnostic email report.
  
  

• Better SHG Extended Focus Image (EFI) images
  SONICC customers will notice better SHG EFI images due to some changes to the EFI algorithm, including reduced noise and inclusion or more “real” signal. The images below show the previous images on the left and the improved images on the right.

Before SHG EFI Improvement                                                                             After SHG EFI Improvement

• Better SONICC laser life
  If the SONICC laser will not be used for two or more hours according to the automatic imaging schedule, the laser will be powered-off until next use to help extend laser lifetime.

 

FRAP

• Full Recovery FRAP data points exported to Rock Maker
  Rock Imager’s ImagerLink now exports additional information about Full Recovery FRAP data points to ROCK MAKER. Future releases of ROCK MAKER will incorporate this additional information -- stay tuned!
  
  

• Additional Full Recovery Intervals
  Rock Imager can now be programmed to take more interval images during Full Recovery imaging sessions. Note that adding additional intervals increases total imaging time.

All ROCK IMAGERs

• Automatic plate definition file backup
  In the interest of protecting and preserving your plate definition files -- which contain vital information about how to image each plate type -- plate definition files are now automatically backed up on a weekly basis.

  
  Recover Plate Definition Dialog Box

• New columns in Imager Event Log
  The Imager Event Log now includes columns for “Inspection ID” and “Imaging Setting”.

  
  Imager Event Log
  

• Excessive time in manual mode alerts
  If ROCK IMAGER is left in manual mode for more than six hours, ROCK IMAGER will email FORMULATRIX support to check on the imager. If the imager was accidentally left in manual imaging, a support technician will return the imager to its automatic imaging schedule, so as not to create a large imaging backlog in the system.

• Improved automated image queue management
  Previously, if someone initiated an "image now" command from ROCK MAKER when ROCK IMAGER is in manual mode, ROCK IMAGER would immediately switch to automatic mode in order to start imaging the plate. Now, the plate will be queued until ROCK IMAGER is switched back into automatic mode, so as not to interrupt manual imaging.

• Individual drop zoom settings for multi-drop plates
  By adding a new control to the Plate Type Editor's Advanced dialog box, we have made it easier to image plates that have multiple drops of different volumes, such as the Intelli-Plate. You can now assign individual zoom settings to each drop at a well.

  
  Set Drop Zoom on a Per-drop Basis
  

• ‘Blob Size’ now in µm
  For ease of interpretation when troubleshooting and tuning drop location, blob sizes are now measured in µm instead of pixels. This change also makes the blob size value independent of image resolution/binning and pixel size.
  

• More precise brightness controls
  In order to increase brightness control precision, the brightness control buttons have been made less sensitive. Now, a single click in the positive or negative direction equals one increment change. Previously, the control was more sensitive, and it was possible to accidentally adjust the control more than desired with a single click.

• ROCK IMAGER software disabled during system diagnostics
  The ROCK IMAGER software is now disabled during system diagnostics to avoid appearing non-responsive. Additionally, a progress bar appears to indicate system status.

 

ROCK IMAGER 1000, 182 and 54

• Automatic laser health monitoring (SONICC dual imagers only)
  ROCK IMAGER product managers will now keep a close eye on the health of the lasers within SONICC systems by reviewing photographs taken of the reference plate under SHG and UV-TPEF light paths in your system on a bi-weekly basis. Images will be emailed to the product manager automatically.

• Load Port scan behavior changes (ROCK IMAGER 1000 only)
  Plates are now left in the load port until further command after initial barcode scanning, allowing you to decide whether to manually image a plate or send it to storage. Previously, all plates were scanned and then picked up for automatic imaging, which created unnecessary delay if you wanted to manually image the plate.

• Visual map of expired plates (ROCK IMAGER 182 and 54)
  Quickly identify the physical location of expired plates in a large visual display. Expired plates are indicated with red text and an EXPIRED label. To view the map, go to the Load Port menu and select View Expired Plates.

  
  Expired Plates in the Load Port

• Monthly expired plate notifications
  Rock Imager can now send monthly notification emails to you reminding you of any expired plates still residing in the imager's storage facilities.

• ROCK MAKER imaging schedule status change (dual imagers only)
  Previously, imaging sessions were reported as "completed" in ROCK MAKER when a plate had been imaged with one light path but was scheduled to be imaged under multiple light paths. Now, plates that have been imaged under one light path and are waiting to be imaged under the second light path will be reported as "imaging" until the plate has been imaged under both light paths.

 

UV and SONICC

• Improved UV to Visible and SONICC to Visible image alignment
  Due to lens distortion, you may have noticed the cursor was only aligned perfectly at the center of a drop when examining image results of different light paths in Compare Mode in ROCK MAKER. This is due to image curvature from lens distortion. In software we now "flatten" the image removing the lens distortion curvature resulting in improved cursor alignment when comparing images from different light paths. The distortion characteristics are unique to each system requiring a simple calibration to be performed to improve image alignment. To take advantage of this improvement, contact support to set up a tuning session.
  

  

  Alignment Improvements

   

• Initial Live Image view fixed (SONICC only)
  Previously, SONICC users would have to turn Live Image on, and then off, and then on a second time in order to see drops correctly. This issue has been fixed, and SONICC users will now see drops displayed correctly the first time Live Image is turned on.

• Laser timeout now resets if stage movement is detected (SONICC only)
  The automatic laser timeout, designed to protect both your samples and laser life, now resets when ROCK IMAGER detects stage movement during manual imaging.

 

ROCK IMAGER 2, FRAP Benchtop and SONICC Benchtop

• Smarter manual mode
  Previously, if you canceled an imaging command made accidentally while in manual mode such as "image plate", you would have to re-scan the plate barcodes to continue imaging. Now, ROCK IMAGER will remember the barcodes and allow you to continue without further interruption.
  

 

FRAP

• Default imaging setting values displayed in Rock Maker
  For greater insight into how images are captured, the default FRAP imaging settings are now displayed in ROCK MAKER. These settings are accessible through the Imaging Settings node of the Explorer.

  
  FRAP Default Imaging Values in ROCK MAKER

• "Top Light" now called "Fluoro Light"
  To make FRAP imaging terms more familiar for new users, the term Top Light has been changed to Fluoro Light.

Before (Left) and After (Right) FRAP Imaging Term Change

 

Outfitting a new lab or expanding a current one?

For those of you in the process of outfitting a new or future lab, a new hardware option is available with visible light imagers. FACIT -- FORMULATRIX Advanced Contrast Imaging Technology -- allows you to control the illumination pattern on a drop in order to see more crystal facets. Any light pattern can be projected onto a drop, including top-left, top-right, bottom-left, bottom-right, darkfield, and brightfield illumination. For more information, see FACIT.

Illumination Options

All ROCK IMAGERs

• 64-Bit compatibility. ROCK IMAGER now supports 64-bit computing for Windows 7 and newer. Due to lack of a suitable 64-bit camera driver, and best efforts to resolve subsequent technical issues, the only way for us to offer 64-bit compatibility is if you decide to purchase a new camera -- which we purchase from a different vendor -- for your imager. Please contact your sales rep for a quote.
  
  

• Improved Drop Location. Behind-the-scenes configuration changes provide you with increased drop location detection accuracy.
  
  

• System usage charts in the Imager Event Log. The Imager Event Log now includes a chart to provide visual feedback about how the imager is being used. You can choose from Plate Type, User Name or Group for the X-axis; the Y-axis displays Usage in Hours. The chart can be saved as an image and data can be exported to Excel. If you have ROCK IMAGER with multiple light paths, you can further organize data by light path. For example, if you have visible and SONICC, your data will be separated into SONICC and visible categories.
  
  

Imager Event Log with Chart

 

• ’Capture Profiles’ renamed to ‘Imaging Settings’. In the interest of making ROCK IMAGER and ROCK MAKER easier for new researchers to use, we’re saying goodbye to capture profiles. While the functionality stays the same, you’ll see the phrase ‘Imaging Settings’ in its place throughout the ROCK IMAGER and ROCK MAKER programs.
  
  

• Windows 8 compatibility. ROCK IMAGER is ready to upgrade to Windows 8 when you are.

 

UV Imagers

• See more microcrystals in UV EFI images. We’ve tweaked some behind-the-scenes settings so that small crystals hidden in dense precipitant are now less likely to be missed when reviewing images. As you can see in the example images below, tiny crystals show up in the new image, but are “smoothed out” and lost in the old image.

Sitting Drop Before UV EFI Improvement

 

Sitting Drop After UV EFI Improvement

 

SONICC Imagers

• Extended SONICC photomultiplier tube (PMT) life through smarter software. If ROCK IMAGER detects too much signal during UV-TPEF or SHG imaging, imaging will automatically stop in order to protect the photomultiplier tube sensors, extending the life of your SONICC imager. If you are using SONICC in manual mode, a message will appear asking you to reduce the laser power. If SONICC is running in automatic mode, the drop producing too much signal will be skipped. If three drops are skipped in a row, then the plate will be skipped for that imaging setting.
  
  

• Additional control over images with a new gain setting. We’ve added new controls to the ROCK IMAGER software so that you can adjust the signal to noise ratio in your images. Previously, gain was set through the configuration files to a default of 5%. You can now lower the threshold if desired, which is beneficial in situations where a drop’s contents generate very-low voltage signal. However, you should expect to see more noise in your images. If you increase the threshold, your images will show less noise, but you sacrifice signal from the drop.

Gain Setting

• Increased Autoscoring accuracy. We're actively working to improve autoscoring for UV/SONICC images. Automatic scoring is a difficult area to perfect. We've taken your feedback about UV/SONICC autoscoring and made some configuration changes. Please continue to give us your feedback so that we can continue to improve this feature!

 

ROCK IMAGER 2 and FRAP BENCHTOP Imagers

• Smarter imaging. You will now be asked which “slot” to image before your imager starts imaging plates without barcodes, saving time and making the software more intuitive. In each imager, slot 1 is on the left and slot 2 is on the right.

ROCK IMAGER 2.11 includes several enhancements to existing features that will make your work easier, as well as image improvements for UV customers, faster plate imaging for ROCK IMAGER 1000 Dual Imager customers due to optimized plate handling, and a faster startup time for SONICC Benchtop customers. FORMULATRIX engineers have also made 27 other changes that won't be obvious to you, but change behind-the-scenes operations for a better overall experience. If you're curious about these additional changes, go to the website to view the latest release notes.

 

All ROCK IMAGERs

• ‘Image Interesting Drops’ from anywhere! Previously, imaging interesting drops required that the plate containing the interesting drops was already at the imaging station. Now, you can find the plate as you normally would, and execute the Image Interesting Drops command from the right-click menu. ROCK IMAGER will move the plate to the imager at the earliest possible time and image your drops. For more information, see Imaging Interesting Drops.
  
  

• See the imaging method for future imaging sessions on the Scheduling tab. We’ve added an ‘Imaging Mode’ column to the Scheduling tab, so you can now more easily see not only when a plate is scheduled to be imaged, but how the plate will be imaged. For more information, see Scheduling Tab.
  
  

  Imaging Modes
  
  

• See how many images RIP is waiting to process. ROCK IMAGER Processor now tells you how many images are waiting to be processed, giving your more insight into behind-the-scenes operations -- and helping you figure out where your images might be if they’re not showing up in ROCK MAKER. For more information, see ROCK IMAGER Processor. Click the image below to enlarge.

  
  

  ROCK IMAGER Processor
  
  

• Clear drop locations -- and their overrides -- from ROCK IMAGER. Now when you clear a drop location in ROCK IMAGER, you will be asked if you also want to clear the drop location override created in ROCK MAKER -- if there is one. For more information, see Clearing Drop Locations. Requires ROCK MAKER 2.9.
  
  

• Include a note when you send log files to support. Sending log files to support to report a freeze or crash? Now you can type in a note to accompany the log file, so we have a better understanding of what you were doing when the incident occurred.

  
  

  Select FIles to Send to FORMULATRIX
  
  

• Behind-the-scenes license checks to keep your ROCK IMAGER software current. ROCK IMAGER now starts checking our servers for renewed license status 14 days before your license is set to expire. If a new license is found, ROCK IMAGER will update your license automatically so that you don't miss any software updates. For more information about licensing, see Licensing.
  
  

• Get your manually scheduled plates imaged, even if ROCK IMAGER shuts down. In previous versions of ROCK IMAGER, if the hardware or software shut down for any reason then manually scheduled plates were lost from memory. Now, ROCK IMAGER remembers all of your manually queued plates, even if your hardware or software crashes, so your manually scheduled plates are still imaged the way you originally planned.
  
  

UV Imaging

• Better image contrast no matter the objective. ROCK IMAGER now attempts to deliver the best contrast when imaging in UV by automatically matching the objective with a certain exposure time.

 

RI 1000 Dual Imagers

• Faster imaging due to better plate handling. Plate handling has been optimized so that there is less downtime between plates -- while the first plate is imaging, ROCK IMAGER will retrieve the next plate and wait for the first plate to finish. Then, it will retrieve the first plate from the imaging station, put the second plate in its place, and return the first plate to its storage location. Meanwhile, imaging has already started on the second plate.

 

SONICC Benchtops

• Faster startup time. The startup sequence for SONICC Benchtop has been optimized so that you can begin using the ROCK IMAGER software while the SONICC laser is warming up. If you attempt to engage the laser for imaging purposes before it is ready, a counter will appear displaying how much more time is needed before SONICC imaging can begin.

ROCK IMAGER 2.10 is a major point release that introduces organizational interface changes, additions to the Plate Configuration page (now called the Plate Type Editor), several enhancements to both the SONICC and FRAP imaging processes, and more. Keep reading to learn about each of the changes.

 

Interface Changes

• New Imager Menu. Various options from the Imager menu have been consolidated into the new Image sub-menu, as shown in the screenshot below.
  

  Imager Menu

• Added the ability to image Interesting Drops. Once you’re running ROCK MAKER 2.8, you will have the ability to tag certain drops as interesting using the “i” key while viewing images in ROCK MAKER. You can then choose to image only interesting drops from the ROCK IMAGER software, saving time and image disk space.

• New Columns on the Scheduling Tab. If you have a dual imager ROCK IMAGER 1000, the Scheduling tab will display two additional columns: Imaging Modes and Completed Imaging. The Imaging Modes column shows imaging methods that were scheduled for an imaging session, and the Completed Imaging column shows imaging methods that were successfully completed. If you are running an automatic imaging session using two imagers, the Imaging Modes column will display the imagers separately. Read more about the Scheduling tab.

  
  

  Scheduling Tab - Automatic Mode

• Improved plate search. We have removed the need to search using “wildcards” – you can now simply type in your search parameters in the appropriate field and press the Enter key to search.

• Easily identify plates that are stationed at an imager. If a plate is currently stationed at the imager, it will appear as highlighted in yellow on any Plates sub-tab (Scheduling, Search, Load Port). Further, we’ve added mouseover explanatory text that explains why a certain plate is highlighted, as shown below. This feature is available for all ROCK IMAGERs except for ROCK IMAGER 2 and Benchtop versions of SONICC and FRAP.

  
  

  Identify Plates

 

Plate Configuration Changes

• Plate Configuration renamed Plate Type Editor. Read more about the Plate Type Editor.

• New Standard Drop Locator field. The Standard Drop Locator field allows you to specify settings related to the number of pixels that should be included in a drop, the aspect ratio, and more.
  

• New Export button. You can now click an Export button to capture your plate settings and save them as an *.xml file. You can then edit the plate definition file in a text editor, rename it, save it, and import it as a new plate definition file using the Browse button next to the Plate Definition field.

  
  

  Standard Drop Location Field

• Enhanced Drop Tuning for SONICC users. The Plate Type Editor has been modified to include a Capture Tuned Drops button, so you can define drop positions with the visible imager, overlay the visible image from each drop position on top of the SONICC live image, and use them as a tuning reference (Dual Imager SONICC only). Read more about drop location tuning.

• Editable Drop Position Coordinates. The X, Y, and Z fields in the Drop Position area are now editable, which means you can input exact drop positions instead of having to use the manual well and drop controls to define drop locations.

 

SONICC Changes

• New Laser Camera Control. A new field has been added to the Camera Control panel allowing you to amplify or reduce the power of the laser at will, expressed as a percentage of maximum power. Read more about camera controls.

  
  

  New Laser Camera Control
  

• Laser automatically turns off when idle. To prevent thermal decomposition to samples, the SONICC laser will now automatically turn off after a specified idle period during manual inspections.

• SONICC arm automatically retracts upon software shutdown. If you exit the ROCK IMAGER software, SONICC will retract its arm to ensure that the plate door is closed when not in use.

 

FRAP Changes

• FRAP Configuration menu improvements. The FRAP Configurations dialog box has been simplified to make setting bleach options, full recovery and high throughput imaging options, and curve-fitting options easier. Read more about FRAP configuration.

• Improved FRAP Capture Profiles. Additional Capture Profile settings are available in ROCK MAKER 2.8, granting you more control over your imaging sessions from the ROCK MAKER side.    

                                                        

  FRAP Capture Profiles

• Improved curve fitting algorithm. FRAP curves are now generated more accurately based on improvements to the curve algorithm.

• Ability to use both Center and Edge bleach spots. You can now choose to select both a Center and an Edge bleach spot when imaging drops.

• Improved setting of Bleach Position Locator. You can adjust specific drop intensity threshold value toward the bleach spots in the FRAP configuration. Read more Configuring FRAP General Options (Full Recovery only).

Auto Scoring

With ROCK IMAGER 2.9, your time spent reviewing images that show empty wells and drops without crystal growth is coming to an end. Based on proprietary algorithms around image intensity, sharpness, edges, and objects, ROCK IMAGER now categorizes each Ultraviolet, UV-TPEF or SHG image as a positive or negative hit. Using this feature, you can choose to filter your images for only positive hits or both positive and negative hits in ROCK MAKER.

The examples below are UV-TPEF images acquired with a SONICC imager. Mousing over the score in ROCK MAKER displays basic information about the score's origin, e.g. "UV-TPEF Auto Score: Positive Hit".

Auto Scoring

You can also filter the Canvas view to show only drops with positive hits from each imager, or drops with a positive hit from any imager. For more information about these capabilities, please see the ROCK MAKER help file.

Based on initial results, our algorithm yields less than 2 % false negatives and less than 8 % false positives. We hope to continually improve our detection algorithms for better accuracy with your help.

Auto Scoring Accuracy
Image Type	Number of Samples	False Positives (%)	False Negatives (%)
Ultraviolet	563	8 %	2 %
SONICC SHG	288	2 %	0 %
SONICC UV-TPEF	576	7 %	0 %

Note: You must be using ROCK MAKER 2.7 to view auto scores.

 

Image Masking

Image Masking can be used to hide fluorescence that appears around the edges of certain plate types containing specific materials. By hiding irrelevant fluorescence, plate masks reduce the probability of a false positive and increase the accuracy of ROCK IMAGER’s auto score capability.

To learn about how to use image masks, see Applying Plate Masks.

 

ImagerLink Changes on ROCK IMAGER 2.9 (ImagerLink v 2.7.0.7)

To complement the autoscoring feature, some options have been added to ImagerLink.

Auto Update

Stay up to date with the latest versions via automatic update. ROCK IMAGER can check for new releases at start up, or you can manually initiate a check at any time from the Help menu.

 

Enhanced Plate Calibration

Camera offsets are now calibrated at four different locations instead of one, resulting in more accurate image overlays between Visible and UV or SONICC images. Support must change some settings to utilize this feature, so please contact us if you find that your offsets between visible and UV are off.

 

Manually Imaging Plates without Barcodes

You can now image a plate without first having to set up an experiment in ROCK MAKER by selecting Load Plate Type from Plate Control or Instant Imaging from the Imager menu.

Load Plate Type in ROCK IMAGER 2 /Benchtop SONICC

 

Instant Imaging

Experiments can be generated directly from ROCK IMAGER with a new feature called Instant Imaging, available from the Imager menu. You can image an entire plate or a few select wells. ROCK IMAGER Processor will send the images to ROCK MAKER. (Requires ROCK MAKER 2.6.)

Read more about Instant Imaging

 

ROCK IMAGER Processor (RIP) Status Displayed on Status Bar

The status bar now conveys information about whether RIP is on or off. RIP should always be running to ensure that images are passed over to ROCK MAKER. Notification emails are also sent out to warn you that RIP is not running.

ROCK IMAGER Processor On

 

Barcode Information Added to the Plate List

You can now search for plates by their barcodes.

Barcode Information in the Plate List

 

Capture Profile Information Viewable in ROCK MAKER

Capture profile information is now available through a new Capture Info Tab in ROCK MAKER, which is especially useful for images taken manually (available in ROCK MAKER 2.5).

Capture Profile

 

ImagerLink v.2.6.0.1

Imager Link changes are of interest only to customers who integrate their own LIMS systems to ROCK IMAGER. These changes are optional, ROCK IMAGER will be backwards compatible to your old implementations if you choose to ignore these.

Read more about the ImagerLink API.

SONICC Laser Automatically Powers Off After Switching to Emergency Power

If there is a power failure and your imager switches over to an alternative power supply, the laser will automatically shut down after a set period of time to prevent damage.

 

Ability to Switch from Current Position in Visible to Same Position in SONICC (New For Dual Imager)

You can now locate an area of interest in visible light and then instruct ROCK IMAGER to show you the same area with the SONICC imager (manual imaging only).

 

Field Of View (FOV) Optic Control Added to All Imagers

You can now set the size of the image through the Zoom control or the new FOV control and the opposite control will automatically populate with the correct values.

FOV in Optics Control

 

ROCK IMAGER Processor (RIP) Improved

Running multiple RIP applications to keep up with image processing tasks? RIP has been modified to meet high processing demand eradicating the need for multiple applications.

 

LCP Drop Location Algorithm More Robust and Reliable

LCP drops lying at the edge of a precipitant are now located by ROCK IMAGER's new algorithm. The size of the drop can be specified in the plate configuration page to make the algorithm more accurate. See the example images below for visual representations of old versus new LCP drop location algorithms.

Drop Size in Drop Location

New and Old Algorithm

 

Using QIAGEN Plates in Your System

Warning messages will now alert you to leave two slots open for Qiagen plates to prevent plate crashes due to different plate dimensions.

Warning Messages for Qiagen Plates

 

User Interface Improvements

The plate configuration dialog box has been updated to reflect the latest algorithm and software changes.

Before	After

User Interface Improvements - Plate Configuration

Up to 40% Decrease in Visible Imaging Time

We have made changes "behind the scenes" to optimize imaging time resulting in a 40% time decrease for 5 MP imaging with Fixed or Auto Exposure brightness settings. 1.2 MP imaging time has decreased by 35%. See the following chart for performance improvement data.

Chart of Imaging Performance on A Full Plate, 96 Well x 1 Drop

Note: The imaging time varies from plate to plate; results vary depending on plate type, camera exposure, resolution and Max Focus settings.

 

Drop Location Positions Saved for Subsequent Inspections

One of the ways we have reduced imaging time is by saving drop location to memory, so the imager can skip that step on subsequent inspections. If you want the imager to define the drop location again, you can clear the drop location from memory on a per-well or per-plate basis on the Scheduling or Plates tab in ROCK IMAGER.

Clear Drop Locations Positions

 

Four Drop Positions in Plate Configuration and Calibration

We have added a H1 drop location position for increased plate imaging accuracy. This change is backwards compatible with previous installs of ROCK IMAGER. The new drop location position will be automatically calculated.

Four Drop Positions in Plate Configuration and Calibration

 

Imager Event Log Table Sorted by Time

All system activities are display chronologically by default.

Time Column in Imager Event Log

 

Automatic Brightness and Laser Power Compensation

You no longer need to reset the exposure after you change the zoom when looking at your drop in manual mode. Laser power now automatically decreases when you zoom in, which is especially useful for ROIs.

The laser power and binning are automatically adjusted when the zoom level changes to provide optimal exposure settings. See the images below for reference.

Automatic Brightness and Laser Power Compensation RI 2.5

Automatic Brightness and Laser Power Compensation RI 2.6

Improved Image Quality for SONICC Images

The Extended Focus Imaging (EFI) algorithm system has been improved to reduce noise, see the images below for comparison.

Before

After

Image Quality for SONICC Images

For more information, see Imaging with SONICC.

 

User Interface Improvements

Before

After

User Interface Improvements - Imager Menu

Display of Plate Owner’s Group

In the Plate Information, the Group field displays the owner's group (as defined in ROCK MAKER -- Requires ROCK MAKER 2.2).

Plate Information

Support for Dual Imagers

ROCK IMAGER can now house two imagers. You can switch between the imagers using the new Imager control drop-down menu located on the right side of the user interface.

Dual Imager in Imager Control

The imager options represent the imagers that are installed in the system. The rest of the imaging control will change based on which imager you select from the Imager Control menu.

In addition, two new options have been added to the Imager menu: Move Plate to Imager Top and Move Plate to Imager Bottom.

 

UV Image Enhancement

The Extended Focus Imaging (EFI) algorithm system used by ROCK IMAGER has been improved in order to reduce noise in the resulting EFI. Below are some samples before (left) and after (right) images.

UV Image Enhancement

 

Event Log

You can now view a report of system events that occur within a specific time period by using the Event Log, which can be found in the Reports menu under the File menu. The Event Log tracks:

1. All plate movements (i.e., movement from the load port to the storage, the storage to the imager, and the storage to the load port).
2. Plate inspection events (scheduled and manually queued).

 

Config File Backup Tool

ROCK IMAGER now automatically backs up all configuration files as part of your database backups. If the imager PC crashes, you can quickly retrieve your backup configuration files. By default, ROCK IMAGER will back up the configuration files once every two weeks.

Config File Backup Tool

 

User Interface Changes

Below are some ROCK IMAGER menus before (left) and after (right) the changes.

Old File Menu	New File Menu
Old Imager Menu	New Imager Menu

1. Save Image menu is moved to the File menu,and Save Image With Scalebar is renamed Save Image menu.

2. View last Visible imageandView last Ultraviolet imagehave been renamed toView Last Image.

3. Move Plate to Storage appears when the plate in the imager is loaded from the load port. Move Plate to Load Port appears when the plate in the imager is loaded from the storage.

4. Best Fit. By default, ROCK IMAGER now shows the “Live Image” window in “Best Fit” mode. ROCK IMAGER can automatically adjust the size of the Live Image screen to fit in the Imager tab. To toggle between Best Fit and Actual Size mode, go to Imager and select Best Fit.

5. View Last Image. It is now easy to view the last image captured from different cameras. Click Imager and select View Last Image, or press CTRL+1. Notification text will appear in the upper-right corner of the image to indicate which camera was used.

Leveling

While manually inspecting a plate, you can adjust the brightness and contrast of an image with the new Leveling Histogram. An auto-leveling feature processes captured images so that the same relative amount of leveling is performed on each image. The leveling histogram dramatically enhances UV images in the following ways:

1. Significantly enhances the brightness and contrast of images.
2. Removes noise from protein in solution and out-of-focus objects.
3. Adds auto-exposure and eliminates the need for capturing images at multiple exposure times.
4. Increases imaging speed by more than a factor of 4.

 

Capture Profiles Based on Imaging Schedules

ROCK IMAGER 2.3 optimizes your imaging schedule by allowing you to use different schedules for different capture profiles. For example, you can run Ultraviolet imaging on the third and seventh day only, as shown in the image below.

Capture Profiles Based on Imaging Schedules

 

Event Notification

ROCK IMAGER can now notify the owner of the plate via email whenever imaging is finished so that you can analyze your latest results.

Notifications are optional and can be sent according to a schedule that you specify. You can select between inspection notifications and digest notifications. Inspection notifications are sent a specified number of minutes after imaging is finished for each plate. Digest notifications are sent once a day and include a summary of daily events.

Notifications emails contain information about the plate’s inspection time, plate ID, barcode, location and current state.

 

Report Menu

ROCK IMAGER can generate a report (in *.txt format) of all the plate types currently in use in the system. The list contains information about the plate type name, the plate definition (whether you used a reference plate when tuning the plate(s) in the system) and the plates' barcode.

 

Management Tools

ROCK IMAGER 2.3 allows you to analyze how different groups are using the imager with the Group column of the Plates tab. To see this column, you must have ROCK MAKER version 2.2 or newer.

Group Column of the Plates Tab

 

RIP Critical Limit

ROCK IMAGER Processor (RIP) will regularly notify you and the FORMULATRIX support team if you are running out of disk space (the notification is sent every 720 minutes by default). In the event that you run out of disk space completely, RIP will suspend itself and periodically check the disk space at a configurable interval. When space becomes available, RIP will automatically resume normal operation.

 

Plate Quotas

ROCK IMAGER 2.3 allows you to manage the number of plates that can be loaded on each imager by assigning quotas to the groups. If a group’s limit is reached, ROCK IMAGER will not allow additional plates belonging to that group to load. Group-based quotas are optional and require ROCK MAKER 2.2 or newer.

Support for Windows 7

ROCK IMAGER now supports Windows 7.

 

Copy to Clipboard

You can now copy the live view image using the copy command keyboard shortcut CTRL+C and paste into your favorite image editor using the paste command keyboard shortcut, CTRL+V.

SMTP Authentication

ROCK IMAGER 2.1.2 now supports authenticated SMTP email used for notifications.

To enable this configuration please set SMTPEnableSSL key in RockImager.config to True.

 

Load Port Order Customization

Users can now customize the order of plates in the load port either from top to bottom or vice versa. To enable this feature, set LoadPortStartLoading key in RobotServices.config to Top or Bottom (the default value is Top).