Application Name	Fibrin Tube Formation
Version	1.0.2
Documentation Version	25.02.2021 - 1
Input Image(s)	2D (standard); RGB and grayscale RGB images are automatically converted to grayscale images
Input Parameter(s)	None
Keywords	fibrin, tube, formation, in-vitro, angiogenesis, vessel, growth, microscopy
Short Description	Detection and quantification of endothelial cell tubes in a fibrin tube 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/pubmed/8601593 and https://www.ncbi.nlm.nih.gov/pubmed/31541300; Reference laboratory: Department of Obstetrics and Gynecology: Dr. Ursula Hiden; Jasmin Strutz, MSc

IKOSA Prisma Fibrin Tube Formation

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 tubes created by endothelial cells in a 3D fibrin matrix, and extracts relevant measures (total tube length, loops, covered area). This analysis is performed within the automatically detected focus area of the image.

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.

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 formats

File formats

1 (Grayscale)

3 (RGB)

RGB images are automatically converted to grayscale images

8 Bit

Min: 256 x 256

Max: 4096 x 4096

typically:
0.80 - 2.85

Image content

Microscopy image of fibrin 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	csv	results.csv A csv file containing the analysis results for the input image.
2	csv	results_01_loops.csv A csv file containing statistics about detected loops.
3	jpg	results_visualization.jpg A visualization of the detection: Out-of-focus area has a red overlay (no analysis is performed in this region). Area covered by cells within the focus region has a blue overlay. Tubes are visualized as green lines. The loops are visualized in pink and labelled with the loop id. The loop id corresponds to the id in results_01_loops.csv. Results visualization Input image Reference: Dr. Ursula Hiden and Jasmin Strutz, MSc, Department of Obstetrics and Gynecology, Medical University of Graz. Please note: the image quality might be reduced for the presentation in the technical docs.

Content

results.csv

Single csv-file

Column NO.	Column name	Examples	Value range	Description

Column NO.	Column name	Examples	Description
1	num_tubes	48	Number of tubes (a tube may have connected sub-tubes).
2	total_tubes_area	56744	Total area covered by tubes in pixels².
3	total_tubes_length	5640	Total length of all tubes in pixels.
4	num_tube_branch_points	122	Number of overall branch points on tubes.
5	num_loops	15	Number of loops.
6	total_loops_area	2126	Total area covered by loops in pixels².

results_01_loops.csv

Single csv-file

Column NO.	Column name	Examples	Value range	Description

Column NO.	Column name	Examples	Value range	Description
1	id	9	1 -	Loop id.
2	area	38	0 -	Area of the loop in pixels².
3	perimeter	22.7	0 -	Perimeter of loop in pixels.

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

1.0.2 Fibrin Tube Formation

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