What's New In Rock Imager 2.14?

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.
  
  
  
  
• 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.
  
  
  
• 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.
  
  
  
• 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.
  
  
• 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.
  
  
• 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.
  
  

 

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.
  
  
• 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.
  
  
  
  
• 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.                                                          
• 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".

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.

 

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.

 

Barcode Information Added to the Plate List

You can now search for plates by their barcodes.

 

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).

 

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.

 

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.

 

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.

 

User Interface Improvements

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

Before	After

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.

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.

 

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.

 

Imager Event Log Table Sorted by Time

All system activities are display chronologically by default.

 

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.

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

For more information, see Imaging with SONICC.

 

User Interface Improvements

Before

After

 

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).

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.

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.

 

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.

 

User Interface Changes

Below are some Rock Imager menus before (left) and after (right) the changes.

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

2. View last Visible image and View last Ultraviolet image have been renamed to View 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.

 

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.

 

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).