Application Name

CAM Assay

Version

3.0.0

Documentation Version

28.09.2021 - 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 format 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.

jpg

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 blue overlay.

• Vessel paths are shown as green lines.

• Vessel branching points are indicated by red dots.

Open

json

roiMeta.json

A json file containing all information regarding the ROIs defined for the analysis job to ensure reproducibility.

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.