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05/13/2008

Blob Tool

The Blob Tool is for counting and sizing objects.

This involves thresholding the image, distinguishing objects from background, using Menu Bar / Colorize / Threshold Slider.  Briefly, you click on an open image to bring it in front, then use Blob Tool / Blob Image / Use Front Image to select the front image as the one to be "blobbed".  Then, use Blob Tool / Blob / Blob to actually blob the image.  Here are examples, giving detailed steps:  Potato (single large particle), Small Particle Count .  More details are here.


 

Blob Buttons & Menus

Description of buttons (commands)

Description of Status Messages

Drawing Buttons and Commands

Stats button details

Stitch & join button details.

top buttons - for setup

 

 

Blob, Statistics and graphics buttons

 

Matching Image button

 

Preprocessing, outline editing, and batch processing buttons.

Examples

Blob graphics

Counting particles exercise

Segmenting a difficult particle.

Measurements from a folder of images.

Spreadsheet from blobs

 

Blobbing without Thresholds

Super Blob Tool.      

Super Blobber Journal Article

 

Batch Processing

Blob Batch Button

Process Folder Tool

Blob or Particle Statistics

List of blob statistics, or measurements
Stats button commands.
Form Factor: defs & illustrations

Notes

 


 

Example of outlines of small particles:

 


Blob Button Details

This color scheme is out of date, but the blobing functions have remained largely the same.


Status Messages in the Blob Tool


Blobbing

The blobbing operation collects and labels contiguous groups of red pixels (chosen with the threshold slider). For example, to size particles, set the threshold so that the particles are red, then use the blob button. ( How to segment an image into blobs.)   Blobs are stored as their outlines in binary files, which are not meant for export to other programs.

Super blobber

This tool segments an image using a ‘super blobbing’ algorithm, which does not require you to choose a threshold.  The algorithm blobs an image starting at the minimum image intensity, and increasing the threshold by a threshold increment. The first blob - the entire image, is gradually split into smaller pieces. See html paper about the algorithm for more details. (The threshold slider is not used or needed for super blobbing.)

Blob Graphics (Drawing)

The graphics drawn by the Blob Tool is not permanent – it disappears when the image is redrawn (R button) or covered by another window and then uncovered. The P button redraws the blob perimeters in different colors and the L button redraws the labels. The Draw button is a menu for drawing various things such as convex hull, perimeters all in one color, diameters, etc.

Explanation of .

 

Stitch and Split

These buttons allow touching particles to be separated, or separate parts of one particle to be joined together.

 

Image Buttons

Three buttons select the images on which the blob tool works.  All three buttons can select the same image - normally this is the case.  Sometimes, however, you may want to to draw blob outlines from one image on another image, or use the intensity information from one image and the blob outlines from a second image to get brightness statistics.

Minimum blob pixel count, or minimum area

Edge?

 

 

Select and Exclude Buttons

The exclude list has blobs that are mostly ignored. All other blobs are outlined, labeled, and in the table of statistics. All non-excluded blobs are called 'good' blobs. The select list has blobs that are selected for special purposes. Only good blobs can be selected. Most operations work on all good blobs. Some also work on selected blobs only, such as: drawing outlines listing statistics showing spectra in PPP window transferring selections to spreadsheet.

Note: Excluded blobs are saved in the file along with the good blobs. The 'Blob / Save to file' command has an option to first remove excluded blobs. Blobs can be saved to individual files if desired.