1.0.1 Fibrin Tube Formation

 

Application Name

Fibrin Tube Formation

Version

1.0.1

Documentation Version

15.05.2020 - 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

Table of contents

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.

 

Content

results.csv

Single csv-file

Column NO.

Column name

Examples

Value range

Description

Column NO.

Column name

Examples

Value range

Description

1

num_tubes

48

0 -

Number of tubes (a tube may have connected sub-tubes).

2

total_tubes_area

56744

0 -

Total area covered by tubes in pixels².

3

total_tubes_length

5640

0 -

Total length of all tubes in pixels.

4

num_tube_branch_points

122

0 -

Number of overall branch points on tubes.

5

num_loops

15

0 -

Number of loops.

6

total_loops_area

2126

0 -

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

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