Application Name

Neurite Outgrowth PC

Version

1.0.0

Documentation Version

15.11.2024 - 1

Input Image(s)

2D (standard and/or WSI) / Time Series / z-Stack / Multichannel Images;

RGB (8 bit), Grayscale (8/16 bit)

Input Parameter(s)

• Regions of interest (optional)

Keywords

Neurite outgrowth, N2a, cell detection, neuritic extensions, morphometry, phase contrast

Short Description

Count and measure morphology parameters of individual neurites and neuronal cell bodies in phase-contrast images.

References / Literature

Klinikum Rechts der Isar, Technische Universität München, Department for Plastic Surgery and Hand Surgery

2D (standard and/or WSI),

Time Series,

Multichannel,

Z-stack*

Check image format

File formats

3 (RGB)

or

1 (Grayscale)

8 Bit

or

16-bit

Max: 6,144 x 6,144

typically: 0.44

Image content

Phase contrast microscopy image of cells.

Additional requirements

None

csv

results.csv

A csv file containing the overall analysis results for the input image or all inclusion ROIs.

csv

results_01_aggregate.csv

A csv file containing the analysis results for all detected aggregates in the input image or inclusion ROIs.

csv

results_02_cell.csv

A csv file containing the analysis results for all detected cells in the input image or inclusion ROIs.

csv

results_03_neurite.csv

A csv file containing the analysis results for all detected neurites in the input image or inclusion ROIs.

jpg

results_vis/vis.jpg (2D image, no ROI), or

results_vis/t<time-step>_z<z-layer>_c<channel>.jpg (for time series, z-stack, or multichannel image, no ROI), or

results_vis/<roi-id>.jpg (2D image, ROI <roi-id>), or

results_vis/t<time-step>_z<z-layer>_c<channel>_<roi-id>.jpg for time series, z-stack, or multichannel image, ROI <roi-id>):

A visualization of the analysis result for a specific time step (of a time series), z-layer (of a z-stack), or channel (of a multichannel image) for either the whole image (if no inclusion ROIs selected for analysis) or each individual inclusion ROI.

Each visualization includes two parts:

• Input

  • input image/ROI

• Segmentation

  • Detected cells are shown in green, aggregates of cells in red and neurites in purple.

  • The skeleton of each neurite, which is a simplified representation of the neurite, is overlayed as a black line

  • object instance index number corresponds to the object_id as listed in the files:

    • results_01_aggregate.csv

    • results_02_cell.csv

    • results_03_aggregate.csv

Open

Open

json

annotation_results.json

A json file that includes geometries of the objects detected in the input image or inclusion ROIs.

json

roiMeta.json

A json file containing all information regarding the ROIs defined for the analysis job to ensure reproducibility. Also, information regarding image and analysis dimensions is provided.

jpg

rois_visualization.jpg or

t<time-step>_z<z-layer>_c<channel>_rois_visualization.jpg

An overview visualization to show locations of all analyzed ROIs for the 2D image or time step <time-step> of a time series, z-layer <z-layer> of a z-stack, or channel <channel> of a multichannel image.

json

jobResultBundleMeta.json

A json file containing all information regarding the analysis job (application name and version, project, etc.) to ensure reproducibility.

1

t

3

1 - 

Time step, i.e. the position of the image in the time series.

2

z

5

1 - 

z-layer, i.e. the position of the layer in the z-stack.

3

c

2

1 - 

Channel, i.e. the position of the channel in the multichannel image.

4

roi_id

ROI-03

ROI-01 - 

<roi-id> starting from “ROI1”. Empty, if no inclusion ROI is specified and the whole image was analyzed.

5

roi_name

“central”

text

Custom text to identify the ROI. Empty, if no inclusion ROI is specified and the whole image was analyzed.

6

roi_size [Px^2]

1212212

1 -

Size of the ROI that was analyzed in pixels^2. The size of the whole image is given if no inclusion ROI is specified and the whole image was analyzed.

7

aggregate_total_num_of_objects

788

1 -

Total number of objects which are detected in the image/ROI.

8

aggregate_on_border_num_objects

12

0 - total_num_objects

Number of objects which are detected in the image/ROI and touch the border of the image/ROI.

9

aggregate_total_area [Px^2]

101863

8 - #pixels

Total area of aggregates which are detected in the image/ROI.

10

aggregate_total_area [%]

0.1

0-100

Total area of aggregates which are detected in the image/ROI, expressed as a percentage of the image/ROI size.

11

cell_total_num_of_objects

788

1 -

Total number of cells which are detected in the image/ROI.

12

cell_on_border_num_objects

12

0 - total_num_objects

Number of cells which are detected in the image/ROI and touch the border of the image/ROI.

13

cell_total_area [Px^2]

101863

8 - #pixels

Total area of cells which are detected in the image/ROI.

14

cell_total_area [%]

0.1

0-100

Total area of cells which are detected in the image/ROI, relative to the size of the image/ROI in percent.

15

neurite_total_num_of_objects

788

1 -

Total number of neurites which are detected in the image/ROI.

16

neurite_on_border_num_objects

12

0 - total_num_objects

Number of neurites which are detected in the image/ROI and touch the border of the image/ROI.

17

neurite_total_area [Px^2]

101863

8 - #pixels

Total area of neurites which are detected in the image/ROI.

18

neurite_total_area [%]

0.1

0-100

Total area of neurites which are detected in the image/ROI, relative to the size of the image/ROI in percent.

1

t

3

1 - 

Time step, i.e. the position of the image in the time series.

2

z

5

1 - 

z-layer, i.e. the position of the layer in the z-stack.

3

c

2

1 - 

Channel, i.e. the position of the channel in the multichannel image.

4

roi_id

ROI-03

ROI-01 - 

<roi-id> starting from “ROI1”. Empty, if no inclusion ROI is specified and the whole image was analyzed.

5

roi_name

“central”

text

Custom text to identify the ROI. Empty if no inclusion ROI is specified and the whole image was analyzed.

6

roi_size [Px^2]

1212212

1 -

Size of the ROI that was analyzed in pixels^2. The size of the whole image is given if no inclusion ROI is specified and the whole image was analyzed.

7

object_id

5

1 -

ID of detected object. More information regarding numbering can be found in Numbering (IDs) of objects in analysis results.

8

is_on_border

“True”

“True” or “False”

Boolean indicator to show if object is touching the border of the image/ROI.

9

object_area [Px^2]

174

8 -

Area of object in pixels^2.

10

bbox_area [Px^2]

304

8 -

Area of bounding box of detected object in pixels^2.

11

area_ratio [%]

0.02

0 - 100

Area of detected object expressed as a percentage of the image/ROI size.

12

perimeter [Px]

53

8 -

Perimeter of detected object in Pixels.

13

circularity

0.78

0 - ~1

Circularity of detected object.

Circularity = 4*pi*area/(perimeter^2).

The circularity of a circle is 1.

14

circularity_ISO

0.65

0 - ~1

Circularity of detected object calculated by ISO definition.

15

solidity

0.97

0 - 1

Solidity of detected object.

Solidity is calculated out of the ratio of an object’s area to the area of its convex hull.

16

eccentricity

0.92

0 - 1

Eccentricity of detected object.

Eccentricity of the ellipse that has the same second-moments as the object area. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. When it is 0, the ellipse becomes a circle.

17

equivalent_diameter [Px]

14

1 -

Equivalent diameter of detected object.

The equivalent diameter is the diameter of a circle having the same area as the detected object.

18

extent

0.57

0 - 1

Extent of detected object.

The extent value is the ratio of the object area to the total bounding box area.

19

minor_axis_length [Px]

9

1 -

Minor axis length of detected object.

The minor axis length is the length of the minor axis of the ellipse that has the same normalized second central moments as the object.

20

major_axis_length [Px]

23

1 -

Major axis length of detected object.

The major axis length is the length of the major axis of the ellipse that has the same normalized second central moments as the object.

21

neurite_total_length [Px]

143.2

0 -

Total length of all neurites in pixels. This is done by calculating the length of the ‘skeleton’, which is a simplified representation of its shape. The skeleton of each neurite can be seen in the visualization.

22

neurites_per_cell

0.0
4.1
””

0 -, or
““

number of neurites divided by the number of individual cells.
The result is ““, in case there are no cells in the image,.

1

t

3

1 - 

Time step, i.e. the position of the image in the time series.

2

z

5

1 - 

z-layer, i.e. the position of the layer in the z-stack.

3

c

2

1 - 

Channel, i.e. the position of the channel in the multichannel image.

4

roi_id

ROI-03

ROI-01 - 

<roi-id> starting from “ROI1”. Empty, if no inclusion ROI is specified and the whole image was analyzed.

5

roi_name

“central”

text

Custom text to identify the ROI. Empty if no inclusion ROI is specified and the whole image was analyzed.

6

roi_size [Px^2]

1212212

1 -

Size of the ROI that was analyzed in pixels^2. The size of the whole image is given if no inclusion ROI is specified and the whole image was analyzed.

7

object_id

5

1 -

ID of detected object. More information regarding numbering can be found in Numbering (IDs) of objects in analysis results.

8

is_on_border

“True”

“True” or “False”

Boolean indicator to show if object is touching the border of the image/ROI.

9

object_area [Px^2]

174

8 -

Area of object in pixels^2.

10

length [Px]

42

Length of the neurite in pixels. This is done by calculating the length of the ‘skeleton’, which is a simplified representation of its shape. The skeleton of each neurite can be seen in the visualization.

11

thickness [Px]

5.3

0 -

Average thickness of the neurite in pixels

12

is_primary_neurite

“True”

“True” or “False”

This flag shows whether a neurite is a "primary neurite." A neurite is considered primary if it is located within 10 pixels of cells or aggregates of cells.

13

bbox_area [Px^2]

304

8 -

Area of bounding box of detected object in pixels^2.

14

area_ratio [%]

0.02

0 - 100

Area of detected object as percentage of overall image area or ROI area inside the image.

15

perimeter [Px]

53

8 -

Perimeter of detected object in Pixels.

16

circularity

0.78

0 - ~1

Circularity of detected object.

Circularity = 4*pi*area/(perimeter^2).

The circularity of a circle is 1.

17

circularity_ISO

0.65

0 - ~1

Circularity of detected object calculated by ISO definition.

18

solidity

0.97

0 - 1

Solidity of detected object.

Solidity is calculated out of the ratio of an object’s area to the area of its convex hull.

19

eccentricity

0.92

0 - 1

Eccentricity of detected object.

Eccentricity of the ellipse that has the same second-moments as the object area. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. When it is 0, the ellipse becomes a circle.

20

equivalent_diameter [Px]

14

1 -

Equivalent diameter of detected object.

The equivalent diameter is the diameter of a circle having the same area as the detected object.

21

extent

0.57

0 - 1

Extent of detected object.

The extent value is the ratio of the object area to the total bounding box area.

22

minor_axis_length [Px]

9

1 -

Minor axis length of detected object.

The minor axis length is the length of the minor axis of the ellipse that has the same normalized second central moments as the object.

23

major_axis_length [Px]

23

1 -

Major axis length of detected object.

The major axis length is the length of the major axis of the ellipse that has the same normalized second central moments as the object.