Application Name

CAM Assay

Version

4.0.0

Documentation Version

03.12.2024 - 1

Input Image(s)

2D (standard and/or WSI) / Time Series / z-Stack / Multichannel Images; RGB or Grayscale (8 bit)

Input Parameter(s)

Regions of interest (optional)

Keywords

CAM, chorioallantoic membrane, in vivo, angiogenesis, chick, vessel, growth, microscopy, assay

Short Description

Quantification of blood vessels on chick chorioallantoic membrane (CAM) assay used in ex-vivo angiogenesis research.

References / Literature

For more information regarding the assay check e.g. https://www.ncbi.nlm.nih.gov/pubmed/19007659 

2D (standard and/or WSI),

Time Series,

Multichannel,

Z-stack*

Check image formats

File formats

3 (RGB)

or

1 (Gray)

8 Bit

WSI formats: arbitrary**

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

typically: 1-7

Image content

Microscopy image of CAM Assay region.

Additional requirements

• Vessel thickness has to be between 3 and 220 pixels.

• Vessels that should be detected have to be in focus.

• Avoid reflections, e.g. by using a polarization filter for imaging.

csv

results.csv

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

csv

results_01_vessels.csv:

A csv file containing statistics about each detected vessel.

jpeg

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

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

results_vis/<roi-id>.jpg (2D image, ROI <roi-id>), or

results_vis/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.

A visualization of the detected vessels contains:

• Areas of detected vessels are shown in a color representing its local thickness.
  The colormap for the thickness is displayed below:

  Open

  

• Vessel paths (skeletons) are shown as black lines.

• Vessel branching points are indicated by white dots.

Open

Results visualization

Reference: Dr. Nassim Ghaffari Tabrizi-Wizsy, Otto Loewi Research Center, Medical University of Graz.

json

annotation_results.json:

JSON file containing detected vessel structures. The position is measured from the left upper corner (1,1) of the image.

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 “ROI-01”. 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_area [Px^2]

3668

0 - #of pixels in image

Total area covered by  detected vessels in Pixel^2.

8

Vessels_total_length [Px]

12092

>=0

Total length of all detected vessels in pixels.

9

Vessels_mean_thickness [Px]

6.98

>0

Mean thickness of detected vessels in pixels.

10

vessels_num_branching_points

776

>=0

Number of detected branching points.

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 “ROI-01”. 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

object_id

1

1 -

branch id.

8

branch_thickness [Px]

5.1243

1-

Average thickness of the branch in pixels.

9

branch_type

1

0, 1, 2 or 3

Type of the branch:

0: endpoint-to-endpoint (isolated branch)
1: junction-to-endpoint
2: junction-to-junction
3: isolated cycle

10

branch_length [Px]

452.3

1 -

Length of the branch in pixels.

It is calculated by taking the length of the skeleton, which is a simplified representation of its shape. The skeleton of each branch can be seen in the visualization.