Details

Name
TEM Collagen Fibril Morphometry
IQbot ID
IQBOT-0035
Version
1.0.0
Research Area(s)
Orthopedics, Common Tools
Processing Time Expectation
Less than 2 Minutes per Image
Acquisition Hardware
Transmission Electron Microscopy
Techniques, Dyes, Stains, & Proteins
Multiple Field TEM
Sample Context
In Tissue
Name
TEM Collagen Fibril Morphometry
IQbot ID
IQBOT-0035
Version
1.0.0
Research Area(s)
Orthopedics, Common Tools
Processing Time Expectation
Less than 2 Minutes per Image
Acquisition Hardware
Transmission Electron Microscopy
Techniques, Dyes, Stains, & Proteins
Multiple Field TEM
Sample Context
In Tissue

Output Parameters

 

This section will identify any output parameters that are only output by the IQbot in its advanced configuration.

 

Total Fibrils
The total number of segmented fibrils in the image.
Mean Area
The mean area of segmented fibrils.
Mean Aspect Ratio
The mean aspect ratio (ratio between the major and minor axes of the best fit ellipse) of segmented fibrils.
Mean Roundness
The mean roundness (perimeter2/(4π*area)) of segmented fibrils (a measure of fibril border roughness or tortuosity).
Mean Diameter
The mean diameter (the average length of diameters passing through the fibril's centroid measured at 2° intervals) of segmented fibrils.
Mean Perimeter
The mean perimeter (the length of fibril border) of segmented fibrils.

 

This section will identify any output parameters that are only output by the IQbot in its advanced configuration.

 

Total Fibrils
The total number of segmented fibrils in the image.
Mean Area
The mean area of segmented fibrils.
Mean Aspect Ratio
The mean aspect ratio (ratio between the major and minor axes of the best fit ellipse) of segmented fibrils.
Mean Roundness
The mean roundness (perimeter2/(4π*area)) of segmented fibrils (a measure of fibril border roughness or tortuosity).
Mean Diameter
The mean diameter (the average length of diameters passing through the fibril's centroid measured at 2° intervals) of segmented fibrils.
Mean Perimeter
The mean perimeter (the length of fibril border) of segmented fibrils.
Area
The area of each fibril segmented.
Aspect Ratio
The aspect ratio (ratio between the major and minor axes of the best fit ellipse) of each fibril segmented.
Roundness
The roundness (perimeter2/(4π*area)) of each fiber segmented (a measure of fibril border roughness or tortuosity).
Diameter
The diameter (the average length of diameters passing through the fibril's centroid measured at 2° intervals) of each fibril segmented.
Perimeter
The perimeter (the length of fibril border) of each fibril segmented.

Image Acquisition


This IQbot was developed to analyze images captured via Transmission Electron Microscopy of collagen fibril cross sections from rabbit MCLs.

 
 

The TEM Collagen Fibril Morphometry IQbot has been built to accommodate the following imaging types only.

   .tif 
  .tiff
  .bmp
 .jpg
.jpeg
 
 

As we reference for IQbots in general here, the TEM Collagen Fibril Morphomery IQbot is only ultimately effective if you upload high quality images for processing. Please ensure that any images you upload follow the below guidelines specific to this IQbot.

High-Resolution:  The quality of the output data you receive is largely dependent on the input image resolution. Please provide high-resolution images to ensure that the IQbot can most effectively differentiate between features.
In-Focus:  Please produce the most in-focus images possible for analysis. Images with high background contrast will result in more accurate and useful data and overlays.
Properly Saturated:  If your submitted images are significantly undersaturated or oversaturated, it is possible that the IQbot will be unable to detect structures, or may group structures together. Please ensure that the images you upload are saturated appropriately.
Clear of Artifacts:  Please take care to avoid creating bubbles, debris, or otherwise inducing artifacts into your image. Such additional features may corrupt the resulting data.
Clear of Accessary Information:  Please do not submit images retaining any annotations, legends, timestamps, or other markings. Every part of the images that you upload will be analyzed and included in the output data.
 
 
 

If you are uncertain whether or not your images meet the quality standards for which this IQbot was validated, or have additional questions relating to image quality, please view our FAQs or contact the ImageQuantify.com support team.

 

     (216) 678-9258           help@imagequantify.com

 

Validation Information


This IQbot has been validated with a Phase I validation process via visual verification. Trained ImageQuantify.com and ImageIQ personnel have determined upon review that the IQbot functions robustly with available test images and accurately provides quantitative information equivalent to that of a manual observer, but with minimal variability and increased breadth of information.

 

The TEM Collagen Fibril Morphometry IQbot quantifies the morphological properties of collagen fibril cross sections in images acquired via Transmission Electron Microscopy. TEM is a valuable imaging tool for nanometer-scale investigation of extracellular matrix organization, as well as for localizing and performing a morphological assessment of subcellular structures. Collagen organization directly impacts the formation and quality of connective tissues. As such, quantitatively describing collagen morphology provides a rigorous method for evaluating the proteins and pathways involved. This robust analysis was originally designed to quantitatively evaluate the spacing, packing, and shape characteristics of imaged collagen fibrils from rabbit medial collateral ligaments (MCLs), but can also be applied to alternative tissues. The IQbot applies various equalization filters, thresholding parameters, and distance-mapping algorithms to segment all individual fibrils in an image. Following segmentation, the analysis produces metrics (i.e., the cross-sectional area, diameter, perimeter, aspect ratio, and roundness) that are measured in terms of both mean values across an image and as values for each fibril. To enable visual verification of IQbot fibril segmentation, a pseudo-colored output image is also generated for each image analyzed, with the individual fibrils outlined in red.

DEMO IMAGE
IQBOT APPLIED IMAGE

 

SAMPLE DATA
Image Total Fibrils Mean Area Mean Aspect Ratio Mean Roundness Mean Diameter Mean Perimeter Area Aspect Ratio Roundness Diameter Perimeter
Sample 1377 7588.089 nm2 1.175 1.081 86.037 nm 287.663 nm 1661.449 nm2 1.587 1.000 43.984 nm 144.292 nm
1376 Additional Rows 1376 Additional Rows 1376 Additional Rows 1376 Additional Rows 1376 Additional Rows