Application Name

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.

2D (standard)

Check image formats

File 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.

csv

results.csv

A csv file containing global analysis results for the input image.

jpg

results_visualization.jpg

A visualization of the analysis:

• lipid droplets are shown in blue,

• mitochondria are shown in red,

• sarcomeres are shown in green

• z-stripes are shown in purple

  • the lengths that were used to measure the z-stripe distances are shown as green lines

• the numbers written within each detected object show the ID of each object. The same IDs are used within the different CSV files.

Open

Results visualization

Open

Input image

Reference: Dr. Dagmar Kolb, Core Facility Ultrastructure Analysis, Medical University of Graz

csv

results_01_lipid_droplets.csv

lipid droplet results

csv

results_02_mitochondria.csv

mitochondria results

csv

results_03_sarcomeres.csv

sarcomere results

csv

results_04_zstripes.csv

z-stripe results

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°)

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.

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.

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.

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.