Application Name	CAM Assay
Version	2.0.1
Documentation Version	07.07.2021 - 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

IKOSA Prisma CAM Assay

You can use this image analysis application or any of our other applications in your account on the IKOSA platform. If it is not on the list of available applications, please contact your organization's administrator or our team at support@ikosa.ai.

Application description

This application automatically segments blood vessels in microscopy images that are taken from chick chorioallantoic membrane (CAM) Assay samples and measures their total area, length, mean thickness and the number of branching points. Vessels that are in the background (lower layers) that appear blurry in the images are not detected. This analysis can also be performed on time-lapse recordings (Time Series), z-stacks, or multichannel images, uploaded as multipage TIFF files.

In the following, the requirements for an accurate analysis are given and the output of the application is described.

Input data requirements

Input image(s)

Input for this application is the following image data:

Image type	Color channels	Color depth (per channel)	Size (px)	Resolution (μm/px)

Image type

Color channels

Color depth (per channel)

Size (px)

Resolution (μm/px)

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.

*Please note: Z-stack images cannot be uploaded into IKOSA but still can be analyzed via IKOSA Prisma API.

**Please note: For images having a dimension larger than 5,000 pixels, skeletonization artifacts occur that may affect the obtained values for length, mean thickness and the number of branching points.

Important:

For all images, the following requirements apply:

The illumination must be constant throughout the image(s).
The sample must be in focus, i.e. no blurry regions in image(s).

Input parameter(s)

No additional input parameters are required for this application.

As an optional parameter, a single or multiple regions of interest (ROIs) can be defined in which the analysis should be performed (‘inclusion ROIs’).

Description of output files and their content

Files

	File format	Description

	File format	Description
1	csv	results.csv A csv file containing the analysis results for the input image or all inclusion ROIs.
2	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.
3	json	roiMeta.json A json file containing all information regarding the ROIs defined for the analysis job to ensure reproducibility.
4	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.
5	json	jobResultBundleMeta.json: A json file containing all information regarding the analysis job (application name and version, project, etc.) to ensure reproducibility.

Content

results.csv

Single csv-file

If one or more time steps (of a Time Series), z-layers (of a z-Stack), or channels (of a multichannel image) were specified, the results in a specific row refer to the time step/z-layer/channel specified in the corresponding column.

If one or more ROIs were specified, the results in a specific row refer to the ROI specified in the corresponding columns, otherwise (empty ROI columns) the results refer to the whole image.

Column NO.	Column name	Examples	Value range	Description

Column NO.	Column name	Examples	Value range	Description
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	Vessels_total_area [Px^2]	3668	0 - #of pixels in image	Total area covered by detected vessels in Pixel^2.
7	Vessels_total_length [Px]	12092	>=0	Total length of all detected vessels in pixels.
8	Vessels_mean_thickness [Px]	6.98	>=0	Mean thickness of detected vessels in pixels.
9	vessels_num_branching_points	776	>=0	Number of detected branching points..

Error information

More information about errors can be found in the Application Error Documentation.

Contact

If you have any questions about this app, as well as suggestions or ideas for new ones, email us at support@ikosa.ai.

Feel free to book a 30-minute meeting to speak with us about IKOSA and the apps!

https://calendly.com/kolaido/book-the-ikosa-platform-demo

IKOSA Knowledge Base

2.0.1 CAM Assay Application Documentation

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