BIOQUANT Feature: Batch Measurement

Description

Batch Measurement is designed to be used with images saved to the disk. It does not go live, control the motorized stage, or capture images. For this functionality, ask about the Automated Imaging Toolkit.

Common batch steps include threshold editing routines (erode, dilate, copy, copy all, cut, paste, fill, invert, mask), measurement routines (preview all, measure all, measure field), navigation routines (next sequential image, next selected array), and script management routines (loop A, loop B, Pause message box).

About the Imaging Toolkit and Batch Measurement
Purchasing the Imaging Toolkit plug-in allows the user to save BIF images (BIOQUANT Image Format). BIF images record the XYZ position of the image and the micron calibration of the image into the image file. When used with stage encoders or a motorized stage this allows the user to capture hundreds of BIF images. When the BIF images are loaded into the Imaging Toolkit, the system is automatically calibrated and stage position is automatically tracked between images. Batch Measurement isused to sequence through the images, performing measurement routines on each image. For automated image capture using a motorized stage, the Automated Imaging Toolkit plug-in can be purchased.

Batch Steps include

• Preview All - On the Auto Measure Object Tab
• Measure All - On the Auto Measure Object Tab
• Measure Field - On the Auto Measure Field Tab
• Load Next Image - On Sequential Image or Imaging Toolkit
• Next Selected Array - On the Select Arrays Selected List
• Erode - Threshold Editing
• Dilate - Threshold Editing
• Paste - Threshold Editing
• Mask - Threshold Editing
• Cut Threshold - Threshold Editing
• Copy Threshold - Threshold Editing
• Fill Closed Object - Threshold Editing
• Copy All - Threshold Editing
• Pause Box - Insert a Pause Box with Message
• Loop A (Start/End) - Insert a Loop and Indicate Repeat Times
• Loop B (Start/End) - Insert a Loop and Indicate Repeat Times

Sample Batch File
This routine automatically measures two cell types per field for twenty images. It pauses between preview and measure to provide the user an opportunity to edit the preview tracing.

This routine assumes you have the Imaging Toolkit. The Imaging Toolkit can read BIF (BIOQUANT Image File) format images. BIF images record the XYZ location of the image and the micron calibration of the image into the image header file. This means that you do not need to calibration for BIF images or indicate that you have changed to an image that represents a new field of view.

This routine can easily be modified to include additional measurement cell types and/or addition images by double clicking the End Loop and increasing the number of loop times. The Pause box could also be removed for a more automated approach, if editing is not necessary.

Command List
Start Loop A
Start Loop B
Erode
Dilate
Preview All
Pause Box: Perform editing...
Measure All
Next Selected Array
End Loop B (2 times)
Load Next Image
End Loop A (20 times)