Application Name	Network Formation Assay
Version	1.0.0
Documentation Version	10.10.2019 - 1
Input Image(s)	2D (standard); RGB and grayscale (RGB images are automatically converted to grayscale images)
Input Parameter(s)	None
Keywords	network, tube, formation, in-vitro, angiogenesis, vessel, growth, microscopy, matrigel
Short Description	Detection of branching points, loops, and cell coverage in network formation assay used for in-vitro angiogenesis research.
References / Literature	For more information regarding the assay check e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230200/; Reference laboratory: Department of Obstetrics and Gynecology: Dr. Ursula Hiden; Jasmin Strutz, MSc;

1 IKOSA Prisma Network Formation Assay
2 Application description
3 Sample data
4 Input data requirements
- 4.1 Input image(s)
- 4.2 Input parameter(s)
5 Description of output files and their content
- 5.1 Files
- 5.2 Content
  - 5.2.1 statistics.csv
  - 5.2.2 statistics_loops.csv
6 Error information
7 Contact

IKOSA Prisma Network Formation 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 the network created by cells in a 2D network (tube) formation assay, typically on an extracellular matrix such as provided as the growth-factor reduced Matrigel® assay, and extracts relevant measures (loops, branching points, covered area).

In the following sections, we provide the necessary input data requirements that are necessary to obtain accurate image analysis results and a description of the output files.

Sample data

To try out this application, sample images can be downloaded here: https://drive.google.com/open?id=1WnUnZr4gbXp6-vpEvPfIa8yBgW_Ko3-P.

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)

Check image format File formats

1 (Greyscale)

3 (RGB)

RGB images are automatically converted to grayscale images

8 Bit

Min: 600 x 600

Max: 6832 x 5124

typically: 1.75

Image content

Microscopy image of 2D network (“tube”) formation assay, typically taken with 4x magnification.

Additional requirements: None

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.

Description of output files and their content

Files

	File format	Description

	File format	Description
1	jpg	segmentation.jpg: An image with the same image dimensions as the input image, showing the segmentation of the tubes/cells. The image contains for each pixel a likelihood for being a tube. Values are in the range between 0 and 255.
2	csv	statistics.csv: A csv file containing statistics about input image.
3	csv	statistics_loops.csv: A csv file containing statistics about detected loops.
4	jpg	visualization.jpg: A visualization of the detection: Branching points are visualized as green circles. The area covered by cells is shown in red. The Loops are visualized using different colors and labelled with L followed by the loop id. The loop id corresponds to the id in statistics_loops.csv.

Content

statistics.csv

Single csv-file

Column NO.	Column name	Examples	Value range	Description

Column NO.	Column name	Examples	Value range	Description
1	branching points	104	0 -	Number of detected branching points.
2	covered area	93869	0 - #of pixels in image	Total area covered by cells or tubes in pixels.
3	num_tubes	190	0 -	Number of Tubes detected.
4	total_tube_length	6641.4	0 - #of pixels in image	Total length of all tubes in pixels.

statistics_loops.csv

Single csv-file

Column NO.	Column name	Examples	Value range	Description

Column NO.	Column name	Examples	Value range	Description
1	id	1	1 -	Loop id.
2	area	10747	0 - #of pixels in image	Area of the loop in pixels.
3	perimeter	452.3	0 -	Perimeter of loop in pixels.

Please note: The parameters marked with an asterisk (*) are calculated using https://scikit-image.org/.

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

1.0.0 Network Formation Assay Application Documentation

Table of contents