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Performing Cell Boundary Analysis for Biomedical Research Using NI LabVIEW 7 Express

Author(s):

Carlos Yapura, G Systems, Inc.; Dave Baker, G Systems, Inc.; Diego Lopez, G Systems, Inc.; Giovanni Sanchez , G Systems, Inc.

Industry:

Life Science

Product:

LabVIEW, Vision

The Challenge:

Developing an integrated solution that interfaces different brands of specular microscopes for image capture, analysis, and reporting using a single software platform as well as developing a cell geometric analysis algorithm while complying with FDA 21 CFR Part 11 regulations.

The Solution:

Creating a custom, LabVIEW-based application to interface with several manufacturers’ specular microscopes using an NI-IMAQ capture board and NI Vision tools to develop a user interface, perform image processing, and execute an analysis algorithm.


image
Screen Shot of the Analysis Module Showing an Overlay of Computed Cell Borders

Creating a Single-Application System
G Systems, Inc. needed to create a system that could capture images from various microscopes using a single application. Previously, we used several software packages to acquire the images and perform analysis. With the new integrated system we created using National Instruments LabVIEW, NI-IMAQ hardware, and NI-Vision software tools provides a single-system solution for image capture, analysis, and reporting on cell geometry. The system enables the end user to compare the results obtained from different microscopes using a single software application platform and performs the analysis tasks more efficiently and accurately than previous systems.

Image Capture Module
We developed the image capture module to run independently from the analysis module so that multiple users can simultaneously perform image acquisition and analysis. With the image capture module, users can acquire images from a single channel at one time from the NI-IMAQ A6822 connector block after defining the active channel in a configuration screen. Because image size and resolution may vary, the image capture module has a built-in calibration procedure so that the user can calibrate a microscope. The user then can manually move cursors on the screen to match the calibration grid on the screen.

Additionally, the user can rotate the image in case the image calibration grid is not aligned with the image coordinate system. The video output from the active microscope is shown live on the screen and the user can snap an image at any time and save it. By implementing third-party image conversion utilities, users can save the images in multiple formats including bmp, tiff, jpg, and png, as well as gif, tga, and pcx. Immediately after saving the image to disk, the CRC value is calculated and stored in the database along with user-selected demographic information. If an image is reacquired, then a version number is also attached to the image filename.

Manual Center Dot Analysis
G Systems developed an independent algorithm to determine the cell borders from user-selected center points. We used tools from the NI Vision Development Module to create the analysis algorithm as well as for user interaction with the image and for overlaying analysis results on the image. The following basic assumptions were used while constructing the analysis algorithm:

1) There is no characteristic cell length parameter. This allows the cell image to contain cells of widely differing sizes.
2) A unique nonintersecting triangular mesh can be drawn connecting the centers of the cells. The initial steps of creating this mesh are outlined as follows:

  • Start with an arbitrary point and its closest neighbor to form a first segment
  • Find the closest point to the first segment to form a first triangle
  • Search outwards from the original triangle

3) A maximum surface angle is specified to determine if a cell next to the border of the mesh is a boundary cell or an inner cell. The maximum surface angle is a configurable parameter. Cell borders can be drawn for inner cells only.

Even though the we created the analysis algorithm using basic assumptions, we recommend recursive checks to ensure geometrical consistency of the triangles in the mesh as well as to determine all of the boundary cells.

Analysis GUI
The user starts the analysis procedure once an image is loaded and displayed on the screen. The user then can select points on the image using a left mouse click and can select any point using the right mouse click either to re-position or delete the selected point. All features work on a zoomed screen as well. An advantage of the current application over other similar applications is that changes to the brightness, contrast, or gamma corrections to the image do not interfere with the analysis procedure. The user also can select the colors of the overlay information that is displayed on the screen. Once the cell analysis is performed, the user can still go to an edit mode that allows him/her to view the triangle mesh and can perform the following editing operations: add/remove an inner cell, change the neighbor relationships between any two cells, and change inner cells to border cells to re-do a recursive surface angle check.

Once the user is satisfied with the analysis results, a report is generated and the results are saved to a database.

Complying with FDA 21 CFR Part 11 Regulations
To comply with the FDA regulations governing electronic records, G Systems developed the system with data integrity as the highest priority. The network administrator set procedures to limit access to network computers, shared drives, and database to authorized personnel only. The following items were then implemented in this application to help preserve data integrity and enable tracking of the data stored:

  • Login screen requires a valid database username and password as well as a privilege setting on the database
  • Time and date stamps are used for recording entries to the database for tracking purposes
  • CRC values for the image files are stored in the database and checked when the images were loaded to ensure file integrity.
  • Version numbers are tagged to images acquired from the same specimen and to repeated analysis reports
  • Reason for change is required for re-calibration or repeated analysis
  • Database triggers enable tracking historical changes in case of an FDA audit


G Systems leveraged the power and versatility of NI off-the-shelf products to create a system that exceeds the capabilities of existing commercial applications and complies with federal regulations.

For more information, contact:
Carlos Yapura
G Systems, Inc.
E-mail: carlos.yapura@gsystems.com