Installation - Photon Machines€¦ · software applications, and CANNOT be recalled into Chromium. This includes data files for use by Iolite and Sequence files used by the Thermo

Photon Machines Inc - Chromium 2.1 New Features and Changes

Revision History• September 17, 2014 – Maintenance release to fix bugs. See page 3 for details.• August 13, 2014 – Maintenance release to update security credentials so that the Notifications work again.• August 4, 2014 – Updated for latest Cr2.1 release. For a description of major new features in this release, see page 3.• June 18, 2014 – Initial release of Cr2.1. For a description of major new features in this release, see page 7.

The following overview describes the major new features and changes that have been incorporated into the new version of the Chromium laser ablation software since the previous release (V2013.8.24). In addition, a list of changes for previous versions of Chromium can be found towards the end of this document, starting on page 22.

InstallationYou do not need to uninstall the old version first – in fact, the old version will need to be present if you are upgrading from a prior version. You can uninstall the old version afterwords if you wish.

You can obtain the Chromium 2.1 updater program at www.photon-machines.com/updates. If you are currently running an older version of Chromium (prior to the initial Chromium 2.0 release), the update may not work and will display an error message. Contact Photon Machines and we will assist you in manually upgrading your system. The updater program does not overwrite any existing files, so all your data files, images etc... are preserved.

Initial Upgrade (from a version prior to Chromium 2.1)No changes to files or settings should be required if you are updating from a previous version of Cr2.1, but if you are upgrading from an older version (prior to the June '14 release of Cr2.1), then you should review the following sections to be aware of some changes.

Configuration File Update

In Chromium 2.1, the format of the configuration file has changed. If you are upgrading from a version prior to Chromium 2.1, then the first time the software is run, it will display a message indicating that it needs to convert the existing Chromium 2.0 configuration file to the new format.

Chromium2.1 Software Addendum Page 1 17 September 2014

http://www.photon-machines.com/updates


The new software requires the new configuration file format, so canceling the update will exit the software.

System ID

The next displayed message prompts for the system serial number and a PIN number. These values are used to establish a secure internet connection for use with the notification and remote control features described later in this document. If you select Cancel now, you can enter these values later from the Settings, System ID / Access Code menu. Note that you must use the System Serial Number from the back of your system, but the Cloud Access PIN number can be any number that you choose.

Camera Orientation

On some systems, the upgrade process causes some camera settings to revert to their default settings. If the camera image appears to be upside down or backwards, you will need to change its orientation. To do this, click the Settings button at the bottom left of the video image area. From the pop up menu, select Video Capture Settings. Then in the resulting window, check or uncheck the Flip Vertical and/or Flip Horizontal check box, then close and restart the software (restarting the software is recommending whenever changing video capture settings).



Cr2.1 September 17 '14 Release – New Features and Fixes• Changed so the software no longer needs to run in Administrator mode.• Fixed a problem with the camera settings for video mirror/flip being reversed.• Fixed a problem with the “Grab Image” button not working after a motor move or scan was aborted.• Fixed a problem with homing motors where a transient signal on a limit switch would cause the homing procedure to never complete.• Fixed a problem with calculating the estimated run time of a scan which would sometimes cause an error when trying to run scans.• Added a button to the “Move Sample” dialog to reset the XY stage position to (0,0).

Cr2.1 August '14 Release – New FeaturesThe following describes the major new features in the August '14 release of Cr2.1. For a list of the other changes and bug fixes, see page 6.

A description of the new features in the June '14 release of Cr2.1 can be found starting on page 7.

Scan List Toolbar ChangesMany of the toolbar buttons have been shortened, to take up less screen real estate. The Recall Experiment and Recall Settings buttons have been combined into a single Recall button, with a dropdown selection for Experiment or Settings. The same is true for the Save buttons.



Note the new option of Export Data under the Save button. The previous Save Experiment button allowed saving a variety of file formats, some of which could be recalled back into Chromium software and some which could not. Now, the Save Experiment option will save formats that CAN be recalled back into Chromium. The Export Data option will save formats used by other software applications, and CANNOT be recalled into Chromium. This includes data files for use by Iolite and Sequence files used by the Thermo Element ICP-MS.

Renaming a group of scansThere is now an easy way to rename a group of highlighted scans, based on their location in the sample chamber. Let’s assume there are a number of scans on a NIST standard, and a number of unknowns to test. Click on the Select/Drag tool in the Scan Tools list, and then use the mouse to drag a box around all the scans on the NIST standard (zoom out as necessary to see them all).

Then click the Rename button in the toolbar at the bottom of the scan list. The Rename Scans window will open, allowing entry of a base name and a starting sequence number. Enter a base name like NIST612-, and a starting number of 1, and press Apply.



The selected scans will then be renamed as NIST612-1 through NIST612-12. Repeat the process for the unknowns, by dragging a selection box around them, clicking the Rename button, and entering a name and starting sequence number.

This provides an easy way to rename scans based on their location in the sample chamber, regardless of what their order might be in the scan list. It is, however, also possible to highlight a group directly in the scan list, and apply the same process.

Show Scan Labels on Image

It is now possible to label the scans displayed in the image map area. The label can come from either the No.( Number) column or the Description column in the scan list. Use the Labels button in the bottom toolbar to toggle labels among Scan Number, Scan Description and Off.

The Labels button can also be used to open the Settings window for Overlay Properties. Under the Scans section, the Text Size option changes the size of the labels. Scan Labels allows



selection of the source of the labels (same as the Labels toolbar button). Label Alignment changes the location of the label relative to the scan: Left, Right, Above or Below the scan.

Save Composite Image MapThe image map as viewed on screen, including overlay scans and images, can be saved to an image file. Expand the Layers/Images part of the image map area, click the Save Map button, and select Export Composite Map. This will open a window allowing the image to be saved to a file. Supported formats are Windows Bitmap (bmp), Jpeg (jpg), and Portable Network Graphics (png).

Drag highlighted scansA group of scans can be moved together, by dragging them in the image map area. Highlight a group of scans, either by selecting them in the scan list, or dragging a box around them in the image map area (when the Select/Drag scan tool is selected). Then hold a keyboard SHIFT key down, click on any of the highlighted scans, and drag the mouse. All highlighted scans will move relative to the mouse movement.

Bug Fixes and Improvements (Cr2.1, Aug '14 Release)In addition to the new features described above, the following bug fixes and changes have been made since the previous (June '14) release of Cr2.1.

• Added a short delay to allow the laser shutter to completely close before doing pre-ablation with the laser output set to 0% (used to warmup the laser).

• Fixed the “Image Grab” button in the Images/Layers toolbar to fix a timing issue that could happen with some cameras, resulting in no image being captured.

• Fixed issue with jogging XY stages when holding down the mouse button that would sometimes cause the stages to back up and reverse or not accelerate smoothly.



• Fixed an issue that could sometimes cause the XYZ stages to not finish homing – made it so software tries to move stages away from limits twice to work around electrically noisy limit switches.

• Fixed an issue where the “SCANS.SETTINGS” command would apply the settings to the pre-ablation pass instead of the ablation pass if the pre-ablation pass tab was selected in the Scan List window. This could sometimes affect the Qtegra laser plug-in operation.

• Fixed a problem where if you entered a system access code with leading zeroes, it didn't get saved properly and you'd be prompted for the access code again the next time the software was started.

• Fixed a problem with the video “flip” and “mirror” settings not getting saved properly.

• Fixed the folder location used by Export Map Data. The Scan data file (*.scancsv) was saved to the same folder as the executable file, rather than the selected folder. (Imported image files were correctly saved to the specified folder.)

• Fixed a problem with image alignment where the alignment would get worse after each attempt to align an image.

New Features (Cr2.1 - June '14 Release)The following describes the major new features that are included in this release. A description of the other changes and bug fixes can be found starting on page 19.

Scan List Changes

Enabled versus Highlighted

The check box column in the scan list is used to identify which scans will be run when the Run Scans button is clicked. If the box is checked, the scan is Enabled, if the box is not checked the scan is Disabled. In the past, any of the scan functions, such as Copy/Move, Translate/Rotate, etc., also applied to those scans that were enabled.

There is now a distinction made between scans that are Enabled and scans that are Highlighted. The scan functions (Copy/Move, etc.) now apply to scans that are Highlighted, regardless of their Enabled state. Note that Highlighted scans are shown with a blue background in the scan list, and the left most column in the list is colored black. (If the scan list window does not have “focus”, the leftmost column may be the only indicator of highlighted state. Clicking the Scan List title bar will return focus to the window, and redisplay the blue highlighted rows.) In the video window, the corresponding scans are also drawn in a highlighted color (blue by default).



Scans can be Highlighted by clicking them in the list. As with most other Windows programs, the Shift key can be used while clicking to highlight a range of scans, and the Control key can be used to highlight multiple but non-consecutive scans. Alternatively, click the Select/Drag tool in the View window, and then use the mouse to click individual scans, or drag a box around a group of scans to highlight all scans within that box. NOTE: In previous versions, this selection box would also Enable the scans (check their check boxes). Now the scans are only highlighted – click the Enable button, or press the space bar to enable the highlighted scans.

List Editing Toolbar

At the bottom of the Scan List window is a toolbar that is helpful in organizing the list of scans. Note that scans are run in same order as they are listed, so changing the order in the list changes the order in which they will be run. The buttons perform as follows:

• All – Highlight all scans in the list. If all scans are already highlighted, clicking it again will unhighlight them all.• Delete – Delete all highlighted scans in the list. A window will pop-up requiring confirmation before actually deleting the scans. NOTE: The keyboard Delete key can also be used to delete highlighted scans.• To Top – Move all highlighted scans to the top of the list (i.e. run these scans first).• To Row – Move all highlighted scans to a specified row. This will pop up a window requesting a row number, and then insert the highlighted scans immediately preceding that row.



• To Bottom – Move all highlighted scans to the bottom of the list (i.e. run these scans last).

Scans can also be moved within the list by dragging them. Use the mouse to highlight multiple scans, then click and hold the left mouse button on an already highlighted scan, and drag to the new desired location. All highlighted scans will then be moved to that location (if they were not consecutive before the move, they will be consecutive after the move).

Tip To delete a group of scans, use the “Select/Drag” tool, and drag a selection box around them, then press the keyboard Delete key.

Experiment and Scan FilesChromium 2.1 now supports saving scans in an “Experiment File” with the extension “.lase”. These files contain all the information needed to exactly duplicate a scan run, including all the trigger and timing settings, preablation/ablation sequencing, laser settings (energy setpoint etc..) and gas mode/flow settings, as well as the scan placement and settings. Internally, these files are in the “INI file” text format.

When you recall an experiment file, you will be prompted for which parts of the file you want to recall – this way, you can selectively recall just the parts you want while preserving your existing settings.

Ablation, Preablation SequencingA new mode has been added which allows for preablation, then ablation to occur separately on EACH individual spot of a line of spots or grid of spots scan. Previously, the entire line or grid of spots would be preablated before the line or grid was then ablated. This option is selected in the Run Scans dialog, as shown here:

Video Scan Highlight ColorScans that are selected either by clicking in the scan list window, or by clicking in the video window are drawn using a Scan Highlight color. This is helpful in visually correlating highlighted scans between the video window and the scan list window.

To change the highlight color, click the “Settings” button in the lower left corner of the video window, and select “Graphic Overlay Settings” from the pop-up menu. In the Scans section of the window, find the row named “Highlighted” and click on the color name to pop up a grid of available colors.



Highlighting Scans via the Video WindowClick the Select/Drag tool to enter the scan highlight mode. Scans can be highlighted by clicking them individually, or drawing a selection box around a group of scans. Normally, clicking an individual scan or drawing a selection box will unhighlight any scans that are already highlighted. However, holding down the keyboard Shift key will keep all existing highlighted scans, and add the newly selected scans to the highlighted group. The keyboard Control key will toggle the highlighted state of any clicked scans or scans inside the box (highlighted will become unhighlighted, unhighlighted will be highlighted).



Note that all scans that are highlighted graphically are also highlighted in the scan list, and can have any of the scan tools applied to them (delete, copy, translate, rotate, etc).

Mosaic Capture LightingThe system camera has always had auto exposure enabled, which usually produces the best lighting for what is in the current field of view. However, this is not ideal when capturing mosaic images, as the lighting changes for each component image, resulting in inconsistent lighting over the whole composite image. For the UEye cameras, there are now settings in the View Controls window that allow disabling auto exposure, and setting the exposure time manually.

Clicking the Build Mosaic button will prompt you to turn off auto exposure. The best quality image will be produced by moving a bright section of the sample into view, and manually setting the exposure such that the video looks good at that location. The resulting mosaic should have good consistent lighting across the whole image. Note that setting the exposure when viewing a darker portion of the sample may cause the brighter portions to wash out in the mosaic.

Remember to re-enable auto exposure for normal sample viewing, after the mosaic is complete.

New Scan PatternsTwo new scan pattern types have been added: the Irregular Area, and the Curve.

Area

Use the Area scan tool to outline an irregular shaped area, and automatically fill the area with line scans.



Each click of the left mouse button will place a point at the mouse cursor location. Click the right mouse button to complete the pattern, and automatically draw a line segment from the last point back to the first point, thereby enclosing the area. Once the pattern is complete, a series of line scans will be automatically calculated to fill the entire area. Changing the Spot Size of the scan will change the number of lines need to fill the area, relative to the diameter of the spot. Use the Select/Drag tool to move any of the defined points to change the area as desired.

Curve

Use the Curve scan tool to place a sequence of points following a curved feature on the sample.



Each click of the left mouse button will place a point at the mouse cursor location. Click the right mouse button to finish the pattern. A curve will be fitted such that it goes through each of the points defined. Use the Select/Drag tool to move any of the defined points to reshape the curve as necessary to match the sample.

New Scan Tools

Scan Review

The Scan Review button opens the Scan Review window, which allows final adjustment of the X, Y and Focus position of all Enabled scans, prior to running those scans. The scan position adjustments can be performed automatically, or manually.

Whether in Automatic or Manual mode, the scan points that can be adjusted are the same points that defined the scan. So for Grids and Rasters, the upper left and lower right corners can be adjusted. For Lines, Lines of Spots, Curves and Areas, each Vertex or endpoint of the scan can be adjusted.



Auto Focus Adjust – The Automatic mode will only adjust the focus position (not the X or Y). Clicking the Start button will automatically step through each enabled scan, and auto focus the scan.

Manual XY and Focus Adjust - The manual method allows manual or automatic adjustment of the focus position, and also allows manual adjustment of the XY position. The manual mode controls are:

Auto Focus after moving to endpoint –If this box is checked, then auto focus will automatically be performed when moving to the next vertex or scan.

Vertex – Move to the next vertex in the current scan. If the current vertex is the last vertex of the scan, then move to the next scan.

Prev – Move to the first vertex of the previous scan.

Next – Move to the first vertex of the next scan, skipping over remaining vertices of the current scan.

Note that as the buttons are clicked, the stages are positioned to the vertex to be adjusted, and that vertex is centered at the crosshair in the video window. The mouse can be used to click and drag the vertex to fine tune the XY position as desired (as long as auto focus is not currently in progress).



Explode Scans

The ability to explode a line of spots or grid of spots into individual spots has existed in previous versions. Now, line based scans such as Rasters, Area scans and multi-segment lines can be exploded into individual line scans.

Exploding the line based scans is useful when generating data files for the Iolite data reduction software. This allows for accurate time stamping in order to correlate stage position data with the Mass Spectrometer count data.

NotificationsMany people run long unattended scans (overnight for example). The software now has the ability to send an email or text message to indicate successful completion of a scan run, or warn of an error during a scan run.

The Notifications can be configured by clicking the Settings menu, and then Notifications. The Notifications window allows entry of multiple email addresses or phone numbers for notification.

Add – Enter an email address or phone number in the entry box, then click the Add button to add to the notification recipient list.



Test – Send a test notification to all email addresses and phone numbers in the notification recipient list.

Remove – Remove the highlighted entry from the notification recipient list.

A notification will be sent when any of the following events occur, and the corresponding check box is checked. The notification message includes the time stamp of when the event occurred.

• Scan Start – a scan run was started.• Scan Done –a scan run was completed successfully.• Scan Abort/Error –a scan run was aborted by a user, or an error occurred.• Information Interlock – a low priority interlock was tripped.• Warning Interlock –a medium priority interlock was tripped (e.g. someone opened the sample drawer).• Error Interlock – a high priority interlock was tripped (e.g. problem with the laser).• Disable All – Checking this box will disable the sending of all notifications until the box is unchecked. (e.g. Disable during the day, while staff members are present, but enable for unattended evening or overnight runs.)

Iolite and CellSpaceThe Iolite software package is able to correlate sample position data from a laser ablation platform with the mass spectrometer count data, assuming both platforms produce the appropriately formatted data files. Additionally, the CellSpace component of Iolite is able to visually overlay the mass spectrometer count data on an image of the sample saved by the laser ablation software.

The following describes how to save the appropriate data files from the Chromium laser ablation software, not how to use Iolite or CellSpace. For information on using Iolite and CellSpace, an excellent tutorial can be found on the Iolite web page: http://ioliteblog.blogspot.com/2012/04/cellspace-images-tutorial.html

Saving the files

The data required by Iolite and CellSpace includes the timestamps and stage positions when the laser is turned on and off. Therefore, the scans must be Run in the Chromium software, in order to generate the data. Once scans have been run, the Iolite compatible files can be stored by clicking the Save Experiment button.


http://ioliteblog.blogspot.com/2012/04/cellspace-images-tutorial.html


In the Save Experiment pop-up window, the Save as type selection must be changed to Iolite Data File.

After the Scan data (called the laser log file by Iolite) has been saved, another pop-up window will appear, allowing selection of images that can be saved for use by CellSpace. Presumably, these would be images from an SEM or other external source, that were imported into Chromium, but could also be Mosaic maps or images captured directly from the system camera.



Resulting files

The Scan data, or laser log file, will be saved as named, with a .csv extension. This is the format necessary for import into Iolite.

Each selected image will be saved as a PNG image file, along with a coord file. The coord file identifies the image location within the sample chamber space, and allows CellSpace to relate the position data in the Scan data file to the image. Note that both the image and coord files are required for import into CellSpace. All image and coord files are prefixed by the scan data name, indicating they relate to the scan data file.

Note Igor, the “host” program for Iolite, has a limit of 31 characters for a wave name. Iolite creates a wave based on the name used for the image coord file (and appends “_wave” to the filename). When saving images, if the name will be too long for Igor, Chromium will truncate the name. As such, the image name may be changed to “ImgXX” where “XX” is a 2 digit number representing the index in the list of image (e.g. MyTest_Img01.coord)

Log XYZ PositionsThe Sequencing and Triggers panel of the Run Scans window has a checkbox for Log XYZ Positions. When this is checked, the XYZ position data and timestamp is stored once every two seconds for Line, Raster, and Area scans, while the scans are running.

After running the scans, this data can be saved by clicking the Save Experiment button, and selecting “Line Scan Data” in the Save as Type box. The resulting file is a text file containing scan parameters for each scan, and a table of the timestamp and position data for each scan.

Thermo Element Sequence FileChromium can export the Scan List in a file format that can be imported by the Thermo Element Mass Spectrometer. This makes it easier to create the sequence in the Element or Qtegra software. To save the file, click the Save Experiment button. In the resulting window, change the Save As Type to “Thermo Element Sequence File”.



Bug Fixes and Improvements (Cr2.1, June '14 Release)The following lists all the main bug fixes and other improvements that have been made in this release.

Performance and Memory Issues Improved speed of “finding devices” when first starting up. Improved speed of saving/recalling scans and experiments. All graphics drawing code has been overhauled to use a new, faster graphics library. Graphics drawing has been optimized to not draw scans/spots etc., which are outside the

field-of-view. Fixed memory “leak” issues when capturing mosaics which could eventually prevent

capturing any new mosaics.

Files and Save/Recall Issues Changed the device configuration file format to INI (SystemConfiguration.ini) instead of

the old DeviceConfiguration.xml file. (Ini files are faster and more robust for this type of application).

Most internal settings are now saved in INI files – settings get automatically imported from old XML files if they exist.

Fixed recalling a map file, such that relative file paths are handled properly. Added periodic logging of XYZ position data to a CSV file while running scans.

(Enabled via the Log XYZ Positions check box in the Run Scans window.) Added a warning when saving scan or experiment files in a format which can't be

recalled (e.g. Iolite format). Fixed problems saving in Iolite format; added a warning when saving in Iolite format but

no data is present (scans must be run to generate data for Iolite). Fixed a problem in selecting images for export into CellSpace.

Limited the length of Iolite image filenames to 26 characters (including the .coord extension). This ensures compatibility with Iolite/Igor for maximum length of a wave name.

Running Scans, Triggers and Timing The accuracy of the estimated time to run a scan has been improved. It now takes stage

and other motor motions into account. Changing the view zoom, tracking, etc., can now be done while running scans. Fixed the save/recall of external trigger (mass spec trigger) settings. This fixes a problem

with triggering on Excite systems. Fixed the external trigger (mass spec trigger) polarity setting so that the new setting takes

effect right away. Fixed the “Reset Actions” button in the Run Scans window to reset the “Shut Down all

Flows” and “Individual Spot Actions” options too. Fixed laser control when running scans with the “Fire Laser” checkbox unchecked, so the

laser remains in the “standby” state, instead of changing to the “enabled” state.



Live Video Display Issues Issues related to video “stalling” (where the live video display would stop updating) have

been resolved. All video capture/display is now synchronized to one thread so that deadlocks and re-entrancy issues should be resolved.

Fixed problems that prevented grabbing an image after a mosaic capture had been canceled.

Added control of automatic exposure and exposure time settings for uEye cameras. Automatic exposure can now be turned off when capturing a mosaic to improve the uniformity of the brightness of the mosaic.

Added buttons to quickly go the “Med” and “Large” zoom levels. Fixed a problem with previously grabbed images, such that “unlocking” and dragging the

image would result in the image being displayed as a solid black rectangle.

Hardware Support Issues Added support for new solid-state ATL laser. Fixed the external trigger (mass spec trigger) such that if the controller device is missing

from the configuration file, it is automatically added (this only needs to be done once). Attenuator on Excite is now always homed at startup to insure proper positioning. Fixed motor homing such that if a motor is outside its travel limits, the limits are disabled

while homing so the stage can move back inside its limits. The sample drawer interlock now disables the laser.

Remote Control InterfaceNote: See the Chromium System Command Set document for details on new commands.

Added “SCANS.INPOS?” command to check if stages are in position to start a scan. Added commands to home the stages and other motors. Added commands to change the PID control gains. Fixed the GAS.MFC command so it indexes the proper MFC (previous index was off-by-

one). Fixed problems with TCP/IP socket connections not closing properly. Added commands to control the optical zoom and lights.

Miscellaneous Issues Fixed laser control so the laser isn’t automatically enabled when beam train purge is

enabled. Fixed the “Laser Enabled” checkbox so it gets updated properly when the laser state

changes. The crosshair, overlays and video no longer “shift around” on the monitor while the

stages are moving. Copying settings from any source to the Laser window now updates the displayed spot

size. Changed the maximum temperature of PID temperature control loop to 5000C. Fixed interlocks so those that were set as “minor” are now “warnings” to prevent them

from interfering with running scans etc.



Reduced the drawing density of rasters and grids when zoomed out (i.e. they are no longer drawn as a solid filled in block).

Changed default beam purge timeout to 600 seconds. Changed the gas mode default setting to go into Purge mode after an Evacuation is done. Fixed a problem in several “grid” controls (scan list, gas valve solenoids), where the

mouse could not select anything in the bottom row of the grid. Light controls no longer have an “On/Off” setting – just set the brightness to 0 to turn off

a light. Fixed the fluence settings in the scan list and laser control windows, so they are updated

when the laser energy setpoint is changed. Fixed the gas flow increments (values used when clicking on the up/down buttons next to

a flow setting) so they are more reasonable. Fixed the software startup process to detect if a copy of Chromium is already running.

Only one copy can run at a time. Fixed the image alignment dialog, so the Cancel button re-applies the old alignment

settings.


Photon Machines Inc - Chromium 2 New Features and Changes

The following describes the changes that were made in Chromium 2 (the version prior to the release of Chromium 2.1).

Chromium2 New Features and ImprovementsChromium2 (or "Cr2") was released as a free upgrade in Feb of 2013. The major differences between Cr2 and older versions are:

• The live video and image map windows have been integrated into a single "targeting" window. In addition to saving room on the display (you no longer need to have both a live video and image map window showing), the new targeting window can show all the scans which are currently defined on the entire sample and allows you to quickly zoom in/out without losing image quality.

• Mosaic images are captured and displayed at high resolution, preserving even small details.

• All images are automatically resampled to improve their appearance at any zoom level.• All images (and live video) can be zoomed in (digital zoom) to better see small features.• Software-based autofocus to find best focus on any sample or surface.• Support for more image formats (Bitmap, JPEG, PNG, TIFF).• New text-based scan file format (uses CSV or "comma separated values") format for fast

and reliable saving/recalling. Files can be easily imported/exported to other software.• New flexible scan run settings to set delays, gas control, and trigger timing to tailor the

run sequencing to meet the needs of almost any experiment.• Numerous bug fixes, stability and performance improvements.

Targeting WindowThe new targeting window is used to place scans, view live video, import, align and view images, and navigate the sample.



Video/Image Display AreaMost of the main targeting window is taken up by the image and video display area. This is where the live video is displayed, along with any images which have been imported and aligned. Crosshairs are drawn to indicate the current position of the laser on the sample. The toolbar along the bottom is used to control the display options.

• STOP – stops the XYZ stage motion.• Joystick Button – used to enable/disable the joystick control. Will be grayed out if no

joystick is connected. Click on the down-arrow to bring up the joystick configuration dialog.

• Mouse Wheel Button – click on the down-arrow button to bring up the mouse-wheel option menu. The mouse wheel can be assigned to either control the image view zoom (digital zoom) or the focus (Z axis position).

• XYZ Position – displays the current laser position. Click on this to bring up the Move Dialog to save/recall positions or move the stages to a specific position or by a specific distance.

• Tracking Button – when pressed, this button enables “tracking mode” in which the current laser position will stay centered in the middle of the display when you zoom in and out. Also, when in tracking mode and the “Move Sample” tool is selected (in the Place/Move Scans toolbar) the laser can be moved around the sample by:1. Clicking the mouse on a location to move the stages to that location, or 2. Holding the left mouse button down to jog the stages (run continuously) until the button is released. The stages will be jogged in the direction of the mouse cursor, relative to the current position of the laser crosshairs. The further away the mouse is from the crosshair position, the faster the stages will be moved.



• Scans Button – click on this button to toggle the displaying of scans overlaid on top of the video and images.

• Zoom: - click on the up/down buttons to change the image view zoom.• Zoom->Video – click on this button to set the zoom level to view the live video at 1:1

scaling (i.e. the video is shown without any digital zoom).

Tips for Navigating the SampleHere are a few quick tips for easily navigating the sample area using the new targeting window:

• If you have a large sample image (or mosaic) loaded and you want to quickly look around the image without actually moving the laser or stages, turn “Tracking” off. Use the mouse wheel to quickly zoom in/out and explore the image.

• With “Tracking” and “Zoom to Video” turned on, you can hold down the left mouse button and use the mouse like a “joystick” to navigate the sample – the stages will move in the direction of the mouse.

• Click on the “XYZ” position display to access the Move dialog box and use the Saved Positions tab to quickly saved a position or move to a previously saved location (see Move Dialog).

Move DialogClick on the XYZ position display to bring up the Move dialog:

Use the Go To/Step tab to move the stages by a specified amount (step mode), or to a specific position. Only the stages which have a check-mark next to them will be moved.

Use the Saved Positions tab to quickly save the current position (by clicking on the Add button), or move to a previously saved position. Select the Move XY Only option if you do NOT want the Z axis (focus) to be moved when you click on the “Move To” action.

Layers/Images PanelClick on the down-arrow to expand the Layers/Images panel and view the layers and images grid:



Layers and Images List

This grid shows all the currently loaded images (and the live video); each image is on its own “layer” where the order of the images/layers in the list corresponds to the order in which they appear on the screen – e.g. the layer at the top is displayed on top of the other layers. You can use the mouse to drag a row in the grid to rearrange the order in which they are drawn on the screen. The following columns are shown:

• Show – use this column to toggle the display of an image or layer.• Locked – when checked, an image is “locked” and can't be moved or sized with the

mouse. If you clear the check mark in this column, then the corresponding image will have a “rubber band” box drawn around it in the main display, and you can use the mouse to drag and re-size the image to align it with the sample. Note that the Live Video layer is always locked.

• Opacity – click in this column to change the transparency of the image or layer.• Layer – description or file name of the image.• Actions – click on an item in this column to:

Goto – moves the stages to position the laser at the center of the corresponding image.Align – brings up the Alignment dialog. (see Image Alignment for more information).Remove – removes the image from the list, but does not delete the image from disk (if the image is a mosaic or image which you have captured, then the software will ask if you want to delete the file from disk).

Layers/Images Toolbar

• Recall Map – recalls a previously saved map. A “map” file contains a list of all the images/layers and their settings and alignments. Note that whenever you close the software it automatically saves the current image map in file called “_DefaultImageMap”.

• Grab Image – captures an image from the live video camera and adds it to the image list.• Build Mosaic – use this to capture and stitch together a set of images over a large area of

the sample. When you click on this button, a “rubber band box” is displayed in the video/image display area; use the mouse to size and position this area to the desired size and location, then click on the Capture Images button and the stages will move around the area and images will be captured. Be sure to focus on the sample first, or all the



images will be out of focus. If the sample is in focus but the images still appear blurry, try increasing the “Settling Time” option to allow the stages to settle into position longer before an image is captured. Note: Mosaic images are automatically put in a folder named “My Pictures/Chromium2/Mosaics”, and the images are saved with a name that corresponds to the current date and time.

• Save Map – click to save the current image map (layer and image list) to a file.• Import Image – click to import and align an image. Supported image types include:

Bitmap, JPEG, PNG and TIFF. See Image Alignment for more information.• Erase – clears out the image map, removing all images from the list, but does NOT delete

any files from disk.• Export Map Files – Saves the current image map, image files, and scans into the selected

folder. This makes it easier to copy images and scans to another system without having to manually find and copy each image, map and scan file.

Image AlignmentIf you have an image of a sample from another source (such as a SEM image, a scanner or a digital camera), you can import it and align it and then use it to target features on the sample. When importing an image, or if you click on the “Align” option in the image list, you will see the following dialog:

If you know the actual physical size of the image (the size of the area on the sample which the image covers), then enter the values in the Width and Height boxes. If you don't know the exact values, you can enter estimated values for now. The center position defaults to the current laser position and is used to specify where in the sample holder the image is positioned – again, if you aren't sure, just leave it at the default value and it can be adjusted later. Once set, click OK and the image will be displayed in the main image area, but will most likely not be precisely aligned with the actual sample until the alignment is refined as explained below.

Rough Image Alignment using the mouseYou can adjust the size and position of an imported image by using the mouse to drag the image to a new position and to re-size the image. In many cases, this will result in an image alignment



which is close enough to allow you to use the image to navigate the sample and locate features. If you need more precise alignment (such as when using the SEM image and you want the image to be exactly aligned with the sample) see the next section (Using Alignment Marks).

To use the mouse to move/size an image, you must first “unlock” the image by clicking on the “Locked” column to remove the check-mark in the Layers and Images List which corresponds to the image being aligned. A “rubber band box” will then be drawn around the image, like this (you may need to zoom out to see the box):

If you position the mouse inside the image and hold the left mouse button down, you can drag the image to a new location. If you hold the mouse down on any of the “control points” (the small white rectangles along the edges of the image), you can drag the edge or corner of the image to change its size. When you are done, click in the “Locked” column to re-lock the image to prevent accidentally moving or resizing the image with the mouse later on.

Precise Image Alignment using Alignment MarksIf you need to precisely align the image with the sample, the best method is to use “Alignment Marks” in which you locate landmarks or features on both the loaded image and the sample, and then let the software calculate the translation, rotation and scaling factors to precisely align the image with the sample.

To begin the alignment procedure, select the “Alignment Mark” tool in the Place/Move Scans toolbox:



Next locate a feature or landmark on the IMAGE and click the mouse (don't worry if the position you clicked on isn't exactly right, you can adjust it later), next find the SAME feature/landmark on the SAMPLE (in the live video window) and click on it to finish placing the first set of alignment marks. Note that you may need to move the stages around to locate the feature on the sample.

Below is an example of using alignment marks to align an image of the sample holder, using one of the screws on the sample holder as a landmark for alignment:

Here's the same view, at a higher zoom:



After you have placed an alignment mark, you can use the “Select/Drag” tool and then click on either of the endpoints of the alignment mark line and fine-tune the placement as needed.

TIP

You may find it easier to place the alignment marks if you purposely start out with the image placed NOT right on

top of the sample that it is being aligned to, but instead slightly offset from it, as is shown in these examples. You can also adjust the opacity (transparency) of the image or the video to help see what is “underneath” the image or

video.

Next repeat this process and place another set of alignment marks. Best results will be obtained if the second set of alignment marks are as far away as possible from the first set. Here's an example where a different mounting screw is being used for aligning the sample holder image:

Again, use the “Select/Drag” tool to fine-tune the placement of the alignment mark endpoints as needed.



You must be sure that the endpoints of each Alignment Mark correspond to the same feature, with the first endpoint being the location of the feature in the IMAGE, and the second endpoint being the location of the feature on the SAMPLE (as viewed with the live video).

Now that two sets of alignment marks have been placed, click on the “Align” action in the “Actions” column which corresponds to the image. A dialog like this will be displayed:

You can click on the “Goto” action to double-check the placement of an alignment mark, or select “Remove” to delete the marks (you will then need to go back and place new marks). If you are satisfied with the placement of the alignment marks, press Apply and the new image alignment will be calculated and the display will be updated. If the new placement looks good, press OK, otherwise press “Reset” to go back to the previous alignment.

Video Focus – Auto Focus

Chromium2 has a new “autofocus” control which is accessed from the “View and Scan Tools” panel located along the left side of the targeting window. Chromium2 uses a proprietary, sophisticated image-processing algorithm to evaluate the focus quality of the live video image. By automatically stepping the Z axis up and down over a user-defined range, the auto focus system is able to find the Z position which has the best focus. The algorithm evaluates the focus in the center part of the image only (approx 20% of the image area, centered on the crosshairs) so it will ignore shadows or aberrations which often occur along the outer edges of the images.

The autofocus algorithm automatically adjusts for differences in lighting conditions and is able to focus on almost any surface – even a clean, transparent surface will work as long as there are at least a few specs of dust or some feature



or scratch on the surface for the algorithm to “lock on to”. The autofocus algorithm will look for the Z position which has the most features in the sharpest focus.

Autofocus is initiated by pressing either the Coarse or Fine search buttons, at which point the software will start moving the Z axis up and down to find the best focus. The autofocus system will only search over the specified range (see below for how to set the ranges), so if the sample is too far out of focus, the autofocus system will not find the best focus.

Once it has found best focus, the autofocus algorithm will terminate and then move the Z axis to that position. You will have to press the Coarse or Fine button again if you want to perform another another autofocus procedure.

There are two autofocus “search modes” – Coarse and Fine. Both modes use the same algorithm, the only difference is the movement range and resolution. Note that when you click on the Coarse button, the autofocus software will automatically perform a Fine mode search when the coarse search is done.

To set up the range and resolution of the autofocus, click on the “gear” button and the following dialog should appear:

In the example above, the Coarse search is set to look for the best focus over a range of 500µm with a resolution of 5 steps, which means the Z axis will be moved +/- 250µm from its current position, in increments of 100µm (500/5=100). Fine search is set to search over a range of 100 (+/- 50µm) with a resolution of 10µm.

You can adjust the range and step count of the search to improve the performance of the system – a wider range may be required if your samples are at different heights; but if you increase the range and don't increase the step count, the resolution will be decreased. However, increasing the step count means the system has to move the Z axis to more positions and analyze more images and so it will take longer.



Live Video WindowOlder versions of Chromium have supported a “Sample View” window which allowed you to view the live video feed from second, low-mag (large field of view) camera, but only worked on system which had two cameras installed. In Chromium2, this window has been replaced by the “Live Video” window which can be used to view the live video from any camera on the system. You can activate this window (if it is not already shown), by selected the “View” menu in the main window, then select “Control Panels->Live Video Window” and window similar to this should be seen:

Along the top of this window is a toolbar with three buttons:

Play – toggles the display of the video on/off.

Setup – opens the video capture settings dialog where you can adjust the camera parameters. (These are advanced and normally do not need to be adjusted).

Source Select – on systems with multiple cameras, use this button to quickly toggle between cameras.



Run Scans ActionsChromium2 includes a much more flexible scheme for setting up the timing and sequencing of a scan run and the associated trigger signals and gas controls. It allows you to set options for both preablation and ablation passes independently, and control when and how triggers are generated or accepted. Once at least one scan is loaded, you can press the Run Scans button (in the Scan List window) and the following window will be displayed (you may have to click on the “v” button at the top-left part of the window to fully expand the display to show all the options). Note that on some systems not all options are available – e.g. Fusions systems have no trigger or gas control options.

The topmost panel selects the ablation/preablation sequencing scheme and trigger polarities as explained below:

Preablation Sequence: Two modes are available – in “Preablate All Scans first” mode, the preablation pass is performed on ALL selected scans BEFORE any ablation passes are performed. Once all the selected scans have been preablated, the ablation pass is next performed on each scan. In “Preablate, then ablate EACH scan” mode, the software will perform the preablation, then the ablation pass on EACH scan before proceeding to the next one.

Note that in the scan list window, the preablation and ablation passes can be enabled or disabled for any individual scan. If any one scan has the preablation or ablation pass disabled, then that pass for that particular scan is skipped.

Deselect Completed Scans: if this option is checked, then once a particular scan has been completed, it is automatically deselected in the scan list. This is useful if you need to interrupt a scan, and then want to restart the run later and have it automatically skip over scans which have already been completed.

Trig In/Out Polarity: selects whether the signals are active-high or active-low. There are hardware jumpers inside the system which select whether a trigger signal



is using a TTL (logic level) voltage, or a contact-closure (relay) interface. Consult the hardware manual for details.

Scan Sequence ActionsThe middle panel contains all the scan sequence “actions” which can be specified. There are two tabs (Preablation and Ablation) – each tab has the same settings available, but the values for each tab can be set differently so that the preablation and ablation action settings can be set independently.

Actions at Start of Preablation/Ablation Pass

At the top are the actions that can be set to happen at the beginning of a pass (either the Preablation or Ablation pass):

• Wait for Trigger In – select this option to have the software pause until the hardware trigger input is received.

• Set Gas Mode – select this option and then pick the desired mode, and the software will then automatically switch to that mode at the start of the pass.

• Activate Trigger Out – select this option and the software will activate the trigger out signal. In addition, on some systems you can select a “Delayed Activation” which means the software will go ahead and continue to execute the scan, but the actual hardware trigger signal will get delayed by the specified amount.

• Pause – specifies a number of seconds for the software to pause. Useful if you need to allow time for gas flows to stabilize etc...

NOTE: If the Preablation Sequence setting is “Preablate ALL Scans First”, then the “Start of Preablation/Ablation Actions” only happen once, at the beginning of each pass, when the first scan is about to be preablated or ablated. If the Preablation Sequence is set to “Preablate, then ablate EACH scan”, then these actions will performed on each and every selected scan pattern in the scan list as each one is preablated and ablated in turn.

Actions for Each Pattern

The next set of actions define what happens right before and right after each scan pattern (line, spot, raster etc..) is ablated or preablated. Normally, “line of spots” and “grid of spots” patterns are treated as a single scan and so the start and end actions are only performed once on each of those patterns, but if the “Do Actions on Each Individual Spot of a Line/Grid of Spots” option is selected, then the Start and End actions are performed on each and every spot of the line or grid of spots, so the in effect the software will treat each spot as if it is a separate scan.

Actions at Start of Each Pattern

Once the preablation or ablation actions have been performed (if any are selected), the software next prepares to actually execute a scan (ie. use the laser to preablate or ablate a spot, line raster pattern etc..). Before the laser is activated and the scan is performed, you can select which



actions to perform. The same actions which are available for the “Start of Preablation /Ablation Pass” are available, and they function the same. The main difference is that these actions (if any are selected) will be performed on each scan pattern (spot, line, raster etc..) just before the laser is activated.

In addition, if a scan pattern has its “Iteration Count” parameter set greater than 1, then a “Pause between Iterations” will be inserted at the end of each iteration (except for the last one) to allow for a delay between iterations if desired.

Actions at End of Each Pattern

Once the lasing is done on a given scan, then another set of actions can be set to happen, before the next scan is processed:

• Clear Trigger Out – deactivate the trigger out signal.• Set Gas Mode – select this option and then pick the desired mode, and the software will

then automatically switch to that mode.• Pause – specifies a number of seconds for the software to pause.

Actions at End of Preablation/Ablation Pass

The same set of actions which are available for the “End of Each Pattern” can be setup to occur at the end of each preablation or ablation pass.

NOTE: If the Preablation Sequence setting is “Preablate ALL Scans First”, then the “End of Preablation/Ablation Actions” only happen once, at the end of each pass, after the last scan has been preablated or ablated. If the Preablation Sequence is set to “Preablate, then ablate EACH scan”, then these actions will performed on each and every selected scan pattern in the scan list after each one is preablated and then ablated in turn.

Shut Off Gas Flows When Done

If this option is selected, then when a scan run is completely finished, the gas flows on all the mass flow controllers will be set to 0. This is useful to save gas when doing long, unattended runs.


Documents

Installation - Photon Machines€¦ · software applications, and CANNOT be recalled into Chromium. This includes data files for use by Iolite and Sequence files used by the Thermo