Scripting for Automation in PAX-it

PAX-it users can benefit from many aspects of the software to streamline their workflow and to make the storage and use of images an easy process. For repetitive operations, PAX-it allows a reproducible method for naming a sequence of measurements, performing an identical analysis from image to image, automatically tagging images with data, and much more.  But were you aware that there is a scripting language available to PAX-it users, so that repetitive, multi-step operations can be performed automatically for you?

The PAX-it Scripting Module is an add-on component that allows a user to build their own scripts related to the operation of a PAXcam, image filing and retrieval functions in PAX-it, motorized stage control, microscope control, image analysis routines, reporting, and much more!  The majority of operations that occur within the PAX-it environment may be scripted, along with standard message boxes and controls, to produce routines that include user prompts, the display of data, loops, conditional branching based on user input, etc.

Here is a small sample of scripts that can be built with the PAX-it Scripting Module:

SCRIPT A:

User is viewing a sample under the scope and would like to capture a series of images at different focal planes and fuse them together into one sharp image. A script button is pressed to perform the rest of the following procedures:

• Start the PAXcam
• Find the proper exposure
• Prompt the user to focus on a plane and press a button to capture the image
• Continues prompting for more images to be captured at different planes, until the user clicks a “Done” button
• Fuse the in-focus information from  each image into a final image
• Save the final image to the QuickSave folder

An alternative script can take advantage of the PAX-it motorized Z (focus) control, prompting the user to identify the topmost and bottommost planes, and then automatically changing the focus through the motor control and capturing the series of images at a specified distance apart!  Of course the image fusion step would also occur, given an even more automated method via a scripted routine defined by the user.

SCRIPT B:

User needs to analyze an large region of interest, comprised of multiple fields of view.  The user places a sample on the scope that is outfitted with a PAXcam and a motorized XYZ stage, and starts the script with a button click.  The following steps proceed automatically:

• Prompt the user to enter a sample number and other relevant information
• Move to a preset ‘start’ position
• Start the PAXcam
• Focus the microscope
• Set the exposure of the camera
• Grab an image and save to a project folder
• Name the folder according to the sample ID given previously by the user
• Enter database information into fields, based on the user’s prior input
• Analyze the image for specific features, according to a stored routine
• Move to the next field of view and repeats the process
• Continue moving one field of view at a time till a preset area has been covered
• Summarize the analysis results from all images from this sample into a report

SCRIPT C:

A sample has 3 different regions that must be screened. The user mounts the sample on a scope with a PAXcam, a motorized stage and motorized lens turret, and starts the script. The script will then:

• Prompt the user to input a sample ID and other relevant data
• Start the PAXcam
• Move the stage to the starting position<
• Pop up a message box with options to start the scan or pause the scan
• Scroll the stage at slow speed, showing the live preview on the PAXcam interface
• If the user pauses the scan: Display controls to move manually and to change objectives
• Pop up a message box with buttons to capture an image, or to return to the location where the stage was paused
• If an image is captured:  Log the coordinates of the stage
• If the scan is resumed:  Return the stage to the last point of scanning, return to the original scan objective, and resumes.
• Upon completion of one region of interest:  Move the stage to the next region
• Upon completion of all the regions:  Pops up a message box allowing the user to enter the name of any study for review
• Returns to the study folder and opens captured images in succession, while returning the stage to the precise coordinates where each image was captured for live inspection.

As can be seen by these short examples, many functions related to image capture, filing, retrieving, analysis, and reporting may scripted, sometimes with additional hardware control to provide an automated method of capturing and analyzing samples.  Place the sample on the scope, start the script, and walk away as the repetitive task is managed by the software.

Scripting is done in VB Script format, allowing standard VB message boxes and functions to be used.  MIS provides sample scripts to illustrate some aspects of the procedure and to get you going with a framework to modify for your needs.