1.0.0 Fibrin Tube Formation
- polina.vinogradova (Unlicensed)
- Philipp Kainz
- Michael Mayrhofer-Reinhartshuber (Unlicensed)
Application Name | Fibrin Tube Formation |
|---|---|
Version | 1.0.0 |
Documentation Version | 07.05.2020 - 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) |
|---|---|---|---|---|
2D (standard)
Check image formats | 1 (Grayscale) 3 (RGB) RGB images are automatically converted to grayscale images | 8 Bit | Min: 256 x 256 Max: 4096 x 4096 | typically: 1.75 |
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 | |
|---|---|---|
| 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:
|
Content
results.csv
Single csv-file
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 |
|---|---|---|---|---|
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!
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