Application Name

CD31 IHC Vessel Quantification

Version

1.0.0

Documentation Version

29.02.2024 - 1

Input Image(s)

2D (standard and/or WSI) / Time Series / z-Stack / Multichannel Images;

RGB (8 bit)

Input Parameter(s)

• Regions of interest (optional)

Keywords

CD31, vessel detection, morphometry, immunohistochemistry, brightfield, vascular density

Short Description

Quantification of CD31 stained blood vessels in IHC brightfield images. The app calculates individual morphology, count, and density of the vessels.

References / Literature

Blond McIndoe Lab, University of Manchester

2D (standard and/or WSI),

Time Series,

Multichannel,

Z-stack*

Check image format

File formats

3 (RGB)

8 Bit

WSI formats: arbitrary

Standard images: max. 25,000 x 25,000

Image content

Brightfield microscopy image of CD31 stained tissue.

Additional requirements

None

csv

results.csv

A csv file containing the overall analysis results for the input image or all inclusion ROIs.

csv

results_01_vessels.csv

A csv file containing the analysis results for all detected blood vessels in the input image or inclusion ROIs.

jpg

results_vis/01_vessels_vis.jpg (2D image, no ROI), or

results_vis/01_vessels_t<time-step>_z<z-layer>_c<channel>.jpg (for time series, z-stack, or multichannel image, no ROI), or

results_vis/01_vessels_<roi-id>.jpg (2D image, ROI <roi-id>), or results_vis/01_vessels_t<time-step>_z<z-layer>_c<channel>_<roi-id>.jpg for time series, z-stack, or multichannel image, ROI <roi-id>):

A visualization of the analysis result for a specific time step (of a time series), z-layer (of a z-stack), or channel (of a multichannel image) for either the whole image (if no inclusion ROIs selected for analysis) or each individual inclusion ROI, for each class number <xx> with class name <class-name> (in training data).

Each visualization includes two parts:

• Input

  • input image/ROI

• Objects

  • object instances are shown as an overlay in random color.

  • object instance index number corresponds to the object_id as listed in the results_01_vessels.csv file.

json

annotation_results.json

A json file that includes geometries of the objects detected in the input image or inclusion ROIs.

json

roiMeta.json

A json file containing all information regarding the ROIs defined for the analysis job to ensure reproducibility. Also, information regarding image and analysis dimensions is provided.

jpg

rois_visualization.jpg or

t<time-step>_z<z-layer>_c<channel>_rois_visualization.jpg

An overview visualization to show locations of all analyzed ROIs for the 2D image or time step <time-step> of a time series, z-layer <z-layer> of a z-stack, or channel <channel> of a multichannel image.

json

jobResultBundleMeta.json

A json file containing all information regarding the analysis job (application name and version, project, etc.) to ensure reproducibility.

1

t

3

1 - 

Time step, i.e. the position of the image in the time series.

2

z

5

1 - 

z-layer, i.e. the position of the layer in the z-stack.

3

c

2

1 - 

Channel, i.e. the position of the channel in the multichannel image.

4

roi_id

ROI-03

ROI-01 - 

<roi-id> starting from “ROI1”. Empty, if no inclusion ROI is specified and the whole image was analyzed.

5

roi_name

“central”

text

Custom text to identify the ROI. Empty, if no inclusion ROI is specified and the whole image was analyzed.

6

roi_size [Px^2]

1212212

1 -

Size of the ROI that was analyzed in pixels^2. The size of the whole image is given if no inclusion ROI is specified and the whole image was analyzed.

7

vessels_total_num_objects

788

1 -

Total number of objects which are detected in the image/ROI.

8

vessels_on_border_num_objects

12

0 - total_num_objects

Number of objects which are detected in the image/ROI and touch the border of the image/ROI.

9

vessels_holes_num_objects

3

0 - total_num_objects

Number of objects which are detected in the image/ROI and have holes (>=1 pixel).

10

vessels_recombined_num_objects

4

0 - total_num_objects

Number of objects which are detected at tile borders of image (tile size: 2048x2048 pixels) and are recombined.

11

vessels_density_num_objects [1/Px^2]

0.0007514953

0 - 1

Total number of objects divided by area of image/ROI.

12

vessels_total_area_objects [Px^2]

101863

8 - #pixels

Total area of objects which are detected in the image/ROI.

13

vessels_density_area_objects

0.0971441268

0 - 1

Total area of objects divided by area of image/ROI.

14

vessels_mean_area_objects [Px^2]

14.324523

8 - #pixels

Mean area of detected objects in Pixels^2.

15

vessels_stddev_area_objects [Px^2]

1.213133

0 - #pixels

Standard deviation of area of detected objects in Pixels^2.

16

vessels_median_area_objects [Px^2]

13.983252

8 - # pixels

Median area of detected objects in Pixels^2.

17

vessels_mean_distance [Px]

13.5016475693

0 -

Mean distance (center-to-center) between detected objects in Pixels. The distance is calculated by the nearest-neighbor distance to other objects of the same type.

18

vessels_stddev_distance [Px]

5.5485792042

0 -

Standard deviation of distances between detected objects in Pixels. The distance is calculated by the nearest-neighbor distance to other objects of the same type.

19

vessels_median_distance [Px]

12.529964086

0 -

Median distance between detected objects in Pixels. The distance is calculated by the nearest-neighbor distance to other objects of the same type.

20

vessels_mean_bbox_area [Px^2]

202.03426395

8 -

Mean area of bounding box of detected objects in Pixels^2.

21

vessels_mean_area_ratio [%]

0.0124492385

0 - 100

Mean area of detected object as percentage of overall  image area or ROI area inside the image.

22

vessels_mean_perimeter [Px]

40.434010152

8 -

Mean perimeter of detected objects in Pixels.

23

vessels_mean_circularity

0.92114213197

0 - ~1

Mean circularity factor of detected objects.

Circularity = 4*pi*area/(perimeter^2).

The circularity of a circle is 1.

Note: Detected objects with a circularity of infinity are ignored when calculating mean_circularity.

24

vessels_mean_circularity_ISO

0.85114213197

0 - ~1

Mean circularity factor of detected objects calculated by ISO defintion.

25

vessels_mean_solidity

0.9310659898

0 - 1

Mean solidity value of all detected objects.

Solidity is calculated out of the ratio of an object’s area to the area of its convex hull.

26

vessels_mean_eccentricity

0.7109644670

0 - 1

Mean eccentricity of all detected objects.

Eccentricity of the ellipse that has the same second-moments as the object area. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. When it is 0, the ellipse becomes a circle.

27

vessels_mean_equivalent_diameter [Px]

11.737309644

1 -

Mean equivalent diameter of all detected objects.

The equivalent diameter is the diameter of a circle having the same area as the detected object.

28

vessels_mean_extent

0.709022842

0 - 1

Mean extent of all detected objects.

The extent value is the ratio of the object area to the total bounding box area.

29

vessels_mean_minor_axis_length [Px]

9.4835025380

1 -

Mean minor axis length of all detected objects.

The minor axis length is the length of the minor axis of the ellipse that has the same normalized second central moments as the object.

30

vessels_mean_major_axis_length [Px]

15.843908629

1 -

Mean major axis length of all detected objects.

The major axis length is the length of the major axis of the ellipse that has the same normalized second central moments as the object.

1

t

3

1 - 

Time step, i.e. the position of the image in the time series.

2

z

5

1 - 

z-layer, i.e. the position of the layer in the z-stack.

3

c

2

1 - 

Channel, i.e. the position of the channel in the multichannel image.

4

roi_id

ROI-03

ROI-01 - 

<roi-id> starting from “ROI1”. Empty, if no inclusion ROI is specified and the whole image was analyzed.

5

roi_name

“central”

text

Custom text to identify the ROI. Empty if no inclusion ROI is specified and the whole image was analyzed.

6

roi_size [Px^2]

1212212

1 -

Size of the ROI that was analyzed in pixels^2. The size of the whole image is given if no inclusion ROI is specified and the whole image was analyzed.

7

bit depth [Bit]

8

8, 16

Bit/color depth of each channel of the image

9

object_id

5

1 -

ID of detected object. More information regarding numbering can be found in Numbering (IDs) of objects in analysis results.

10

object_center_x

741

1 - image/ROI width

x-coordinate of object center (centroid, starting from upper left corner, along image/ROI width).

11

object_center_y

26

1 - image/ROI height

y-coordinate of object center (centroid, starting from upper left corner, along image/ROI height).

12

is_on_border

“True”

“True” or “False”

Boolean indicator to show if object is touching the border of the image/ROI.

13

has_holes

“False”

“True” or “False”

Boolean indicator to show if object has holes (>=1 pixel).

14

is_recombined

“False”

“True” or “False”

Boolean indicator to show if object was recombined because it was detected at tile borders of image (tile size: 2048x2048 pixels).

15

object_area [Px^2]

174

8 -

Area of object in pixels^2.

18

distance_nearest_neighbor [Px]

22.090722034

0 -

Distance (center-to-center)  to the nearest other object of the same class in pixels.

19

bbox_area [Px^2]

304

8 -

Area of bounding box of detected object in pixels^2.

20

area_ratio [%]

0.02

0 - 100

Area of detected object as percentage of overall image area or ROI area inside the image.

21

perimeter [Px]

53

8 -

Perimeter of detected object in Pixels.

22

circularity

0.78

0 - ~1

Circularity of detected object.

Circularity = 4*pi*area/(perimeter^2).

The circularity of a circle is 1.

23

circularity_ISO

0.65

0 - ~1

Circularity of detected object calculated by ISO definition.

24

solidity

0.97

0 - 1

Solidity of detected object.

Solidity is calculated out of the ratio of an object’s area to the area of its convex hull.

25

eccentricity

0.92

0 - 1

Eccentricity of detected object.

Eccentricity of the ellipse that has the same second-moments as the object area. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. When it is 0, the ellipse becomes a circle.

26

equivalent_diameter [Px]

14

1 -

Equivalent diameter of detected object.

The equivalent diameter is the diameter of a circle having the same area as the detected object.

27

extent

0.57

0 - 1

Extent of detected object.

The extent value is the ratio of the object area to the total bounding box area.

28

minor_axis_length [Px]

9

1 -

Minor axis length of detected object.

The minor axis length is the length of the minor axis of the ellipse that has the same normalized second central moments as the object.

29

major_axis_length [Px]

23

1 -

Major axis length of detected object.

The major axis length is the length of the major axis of the ellipse that has the same normalized second central moments as the object.