1.0.0 TEM Myocardium Assay
Application Name | TEM Myocardium Assay |
---|---|
Version | 1.0.0 |
Documentation Version | 15.03.2020 - 1 |
Input Image(s) | 2D (standard); RGB and grayscale, 8 bit or 16 bit. RGB images are automatically converted to grayscale images. |
Input Parameter(s) | None |
Keywords | cardiovascular, ex-vivo, myocardium, organelle, mitochondria, lipid droplet, sarcomere, z-stripe, microscopy, transmission electron microscopy, tem |
Short Description | Segmentation of mitochondria, lipid droplets, sarcomere, and z-stripes in myocardial tissue sections imaged by transmission electron microscopy. |
References / Literature | Reference laboratory: Core Facility Ultrastructure Analysis Graz: Dr. Dagmar Kolb. |
Table of contents
- 1 IKOSA Prisma TEM Myocardium 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 results.csv
- 5.2.2 results_01_lipid_droplets.csv
- 5.2.3 results_02_mitochondria.csv
- 5.2.4 results_03_sarcomeres.csv
- 5.2.5 results_04_zstripes.csv
- 6 Error information
- 7 Contact
IKOSA Prisma TEM Myocardium 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 and measures different types of structures (mitochondria, lipid droplets, sarcomere, z-stripes) in myocardial tissue sections imaged by transmission electron microscopy. The application was developed and tested with images of myocardial tissue sections of mice.
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://www.kolaido.com/wp-content/uploads/2020/07/kmlvision-ikosa-sample-images-for-tem-myocardium-assay.zip
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 | 3 (RGB) 1 (Grayscale)
RGB images are automatically converted to grayscale images | 8 Bit or 16 Bit | Min: 512 x 512 Max: 6144 x 6144 | typically: 3-6 |
Image content Transmission electron microscopy image of myocardial tissue section. Additional requirements Before imaging, the sample is embedded in synthetic resin, then sliced into ultra-thin sections of approximately 70 nm. Platin blue and lead citrate are used for contrasting. |
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 global analysis results for the input image. |
2 | jpg | results_visualization.jpg A visualization of the analysis:
Results visualization Input image Reference: Dr. Dagmar Kolb, Core Facility Ultrastructure Analysis, Medical University of Graz Please note: the image quality might be reduced for the presentation in the technical docs. |
3 | csv | results_01_lipid_droplets.csv lipid droplet results |
4 | csv | results_02_mitochondria.csv mitochondria results |
5 | csv | results_03_sarcomeres.csv sarcomere results |
6 | csv | results_04_zstripes.csv z-stripe results |
Content
results.csv
Single csv-file
Column NO. | Column name | Examples | Value range | Description |
---|---|---|---|---|
1 | Lipid Droplets - count | 5 | 0 - | number of lipid droplets |
2 | Lipid Droplets - total area [Px^2] | 5432 | 0 - | total area covered by lipid droplets in Pixel^2 |
3 | Lipid Droplets - total area [%] | 2.523 | 0 - 100 | total area covered by lipid droplets in % of image size |
4 | Lipid Droplets - completely within image - count | 4 | 0 - | number of lipid droplets that are completely within the image (i.e. instances that do not touch the image borders) |
5 | Lipid Droplets - completely within image - total area [Px^2] | 1321 | 0 - | total area covered by lipid droplets that are completely within the image (i.e. instances that do not touch the image borders) in Pixel^2 |
6 | Lipid Droplets - completely within image - total area [%] | 1.245 | 0 - 100 | total area covered by lipid droplets that are completely within the image (i.e. instances that do not touch the image borders) in % of image size |
7 | Mitochondria - count | 5 | 0 - | number of mitochondria |
8 | Mitochondria - total area [Px^2] | 5432 | 0 - | total area covered by mitochondria in Pixel^2 |
9 | Mitochondria - total area [%] | 2.523 | 0 - 100 | total area covered by mitochondria in % of image size |
10 | Mitochondria - completely within image - count | 4 | 0 - | number of mitochondria that are completely within the image (i.e. instances that do not touch the image borders) |
11 | Mitochondria - completely within image - total area [Px^2] | 1321 | 0 - | total area covered by mitochondria that are completely within the image (i.e. instances that do not touch the image borders) in Pixel^2 |
12 | Mitochondria - completely within image - total area [%] | 1.245 | 0 - 100 | total area covered by mitochondria that are completely within the image (i.e. instances that do not touch the image borders) in % of image size |
13 | Sarcomeres - count | 5 | 0 - | number of sarcomeres |
14 | Sarcomeres - total area [Px^2] | 5432 | 0 - | total area covered by sarcomeres in Pixel^2 |
15 | Sarcomeres - total area [%] | 2.523 | 0 - 100 | total area covered by sarcomeres in % of image size |
16 | Sarcomeres - completely within image - count | 4 | 0 - | number of sarcomeres that are completely within the image (i.e. instances that do not touch the image borders) |
17 | Sarcomeres - completely within image - total area [Px^2] | 1321 | 0 - | total area covered by sarcomeres that are completely within the image (i.e. instances that do not touch the image borders) in Pixel^2 |
18 | Sarcomeres - completely within image - total area [%] | 1.245 | 0 - 100 | total area covered by sarcomeres that are completely within the image (i.e. instances that do not touch the image borders) in % of image size |
19 | Z-Stripes - count | 5 | 0 - | number of Z-Stripes |
20 | Z-Stripes - total area [Px^2] | 5432 | 0 - | total area covered by Z-Stripes in Pixel^2 |
21 | Z-Stripes - total area [%] | 2.523 | 0 - 100 | total area covered by sarcomeres in % of image size |
22 | Z-Stripes - completely within image - count | 4 | 0 - | number of Z-Stripes that are completely within the image (i.e. instances that do not touch the image borders) |
23 | Z-Stripes - completely within image - total area [Px^2] | 1321 | 0 - | total area covered by Z-Stripes that are completely within the image (i.e. instances that do not touch the image borders) in Pixel^2 |
24 | Z-Stripes - completely within image - total area [%] | 1.245 | 0 - 100 | total area covered by Z-Stripes that are completely within the image (i.e. instances that do not touch the image borders) in % of image size |
25 | Z-Stripes - mean distance [Px] | 327.0 | 0 - | Mean distance between Z-Stripes (i.e. the mean length of sarcomeres) in Pixels. This parameter is only estimated in transverse muscle sections. The distance between Z-stripes is estimated by finding Z-stripes that are parallel (+/- 30°) |
results_01_lipid_droplets.csv
Single csv-file
Column NO. | Column name | Examples | Value range | Description |
---|---|---|---|---|
1 | id | 1, 2, 3, ... | 1 - | id of each lipid droplet |
2 | area [Px^2] | 1532 | 1 - | area of each lipid droplet in Pixel^2 |
3 | area [%] | 1.95 | 0 - | area of each lipid droplet in % of image size |
4 | completely within image | yes | {yes, no} | yes if the lipid droplet is completely within the image (i.e. the lipid droplet does not touch the border), otherwise no. |
results_02_mitochondria.csv
Single csv-file
Column NO. | Column name | Examples | Value range | Description |
---|---|---|---|---|
1 | id | 1, 2, 3, ... | 1 - | id of each mitochondria |
2 | area [Px^2] | 1532 | 1 - | area of each mitochondria in Pixel^2 |
3 | area [%] | 1.95 | 0 - | area of each mitochondria in % of image size |
4 | completely within image | yes | {yes, no} | yes if the mitochondria is completely within the image (i.e. the mitochondria does not touch the border), otherwise no. |
results_03_sarcomeres.csv
Single csv-file
Column NO. | Column name | Examples | Value range | Description |
---|---|---|---|---|
1 | id | 1, 2, 3, ... | 1 - | id of each sarcomere |
2 | area [Px^2] | 1532 | 1 - | area of each sarcomere in Pixel^2 |
3 | area [%] | 1.95 | 0 - | area of each sarcomere in % of image size |
4 | completely within image | yes | {yes, no} | yes if the sarcomere is completely within the image (i.e. the sarcomere does not touch the border), otherwise no. |
results_04_zstripes.csv
Single csv-file
Column NO. | Column name | Examples | Value range | Description |
---|---|---|---|---|
1 | id | 1, 2, 3, ... | 1 - | id of each z-stripe |
2 | area [Px^2] | 1532 | 1 - | area of each z-stripe in Pixel^2 |
3 | area [%] | 1.95 | 0 - | area of each z-stripe in % of image size |
4 | completely within image | yes | {yes, no} | yes if the z-stripe is completely within the image (i.e. the z-stripe does not touch the border), otherwise no. |
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.
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