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 Patching blob outlines. Convex Hull and caliper diameters Perimeter Nearest neighbors.

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This color scheme is out of date, but the blobing functions have remained largely the same.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

• Blob Image Click to select image to blob.
• Draw Image Click to select image on which to draw boundaries, labels.
• Data Image Click to select image for intensity data. (The same image can be used for all three above functions. Clicking selects the front image window.)

• Min area!
  • Blobs below this area (number of pixels)are ignored. Useful for eliminating noise.
  • Set this to be 1 less than the area of the smallest particle or object that you intend to measure.

• Allow blobs to touch edge of image or not.
  • (Note - Superblobber blobs always allowes touching edge of image.)
  • NOTE: The blobber trims off a one pixel border before doing anything else. These pixels are lost. So if blobs are not allowed to touch the edge of the image, all red pixels must actually be TWO pixels away from the edge.
  • If you are measuring large particles that are cropped by the edge of the image obviously only a little, then allow the blobs to touch the edge of the image. Otherwise no blob statistics will be available for that particle. (Given the one pixel border throw-away, this means the red pixels can then be within one pixel of the image edge.)

• Exclude Exclude blobs Selects blobs by index for exclusion or 'hiding'. Also shows any selected statistics for that blob.
• Undo excluded blobs Restores excluded blobs.
• Remove excluded blobs Permanently removes blobs. Cannot be restored.