Application Name

Version

3.0.0

Documentation Version

25.01.2024 - 1

Input Image(s)

2D (standard and/or WSI) / Time Series / z-Stack / Multichannel Images; RGB or Grayscale (8-bit, 16-bit)

Input Parameter(s)

Regions of interest (optional)

Keywords

wound, healing, scratch, in-vitro, directional cell migration, migration rate, regeneration, proliferation, growth, microscopy

Short Description

Detection and measurement of the (artificial) gap, the “scratch,” on a confluent cell monolayer for in-vitro wound healing research.

References / Literature

For more information regarding the assay check e.g. https://pubmed.ncbi.nlm.nih.gov/15576902/ or https://www.nature.com/articles/nprot.2007.30 ;

2D (standard and/or WSI),

Time Series,

Multichannel,

Z-Stack*

Check image formats

File formats

3 (RGB)

or

1 (Gray)

8 Bit

or

16 Bit

Standard images and WSI formats:

Max: 6144 x 6144

typically: 0.3-1.16

Image content

Microscopy (phase contrast or brightfield) image of a cell monolayer showing an (artificial) gap with no cells, typically taken with 10x magnification.

Additional requirements

• The measurement of scratch width is only supported for images showing a single (not multiple) scratch.

csv

results.csv:

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

Description for visualizations:

• Areas and contours

  • no color: scratch area (the largest uncovered area)

  • green: cells and cell-covered area

  • red: bubbles (=cell-free areas outside the scratch)

  • cyan: free/floating cells and cell aggregates inside of scratch

• Lines

  • magenta: Two Parallel lines fitted to scratch “frontlines”, only calculated when the cell-covered area borders are not yet touching anywhere.

Open

Results visualization

Open

Input images

Reference: Zaritsky A; Natan S; Kaplan D; Ben-Jacob E; Tsarfaty I (2015): Supplemental materials for "Live time-lapse dataset of in vitro wound healing experiments." GigaScience Database. http://dx.doi.org/10.5524/100118

json

annotation_results.json:

JSON file containing detected cells (cell covered regions). The position is measured from the left upper corner (1,1) of the image.

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 “ROI-01”. 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

total_area_without_scratch [Px^2]

1011878

0 - #of pixels in image

Total area without scratch in Pixel^2, includes cell-covered area, free/floating cells and bubbles (= cell-free areas outside the scratch).

8

total_area_without_scratch_ratio [%]

68.6

0 - 100

Ratio of total area without scratch to the total area of the image.

9

scratch_area [Px^2]

36698

0 - #of pixels in image

Total scratch area (cell-free area in center of image) in Pixel^2. Free/Floating cells inside of scratch are not considered part of the scratch.

10

scratch_area_ratio [%]

31.4

0 - 100

Ratio of scratch area to total area of image. Free/Floating cells inside of scratch are not considered part of the scratch.

11

scratch_area_incl_free_cells [Px^2]

37580

0 - #of pixels in image

Total scratch area (cell-free area in center of image) in Pixel^2. Free/Floating cells inside of scratch are considered part of the scratch.

12

scratch_area_incl_free_cells_ratio [%]

31.6

0 - 100

Ratio of scratch area to total area of image. Free/Floating cells inside of scratch are considered part of the scratch..

13

scratch_width_area [Px]

400.5

>=0

Scratch width in Pixel, calculated by dividing the scratch_area by the “total length” of the scratch, i.e. the maximum distance between two points on the scratch border. Maximum value depends on the scratch orientation.

14

scratch_width_frontlines [Px]

435

>=0 

Scratch width in Pixel, estimated by mean distance between the two linearly fitted “frontlines” (scratch borders).Value is 0, if no frontlines have been fitted. Maximum value depends on the scratch orientation.

15

is_scratch_closed

0

0 or 1

Boolean indicator if scratch is closed (1) or not (0).

16

cells_covered_area [Px^2]

22143

0 - #of pixels in image

Total area of cell-covered region in Pixel^2. Bubbles (= cell-free areas outside the scratch) are not included in this area.

17

cells_covered_area_ratio [%]

68.6

0 - 100

Ratio of cell-covered area to total area of image. Bubbles (= cell-free areas outside the scratch) are not included in this area.

18

cells_covered_area_incl_bubbles [Px^2]

23053

0 - #of pixels in image

Total area of cell-covered region in Pixel^2. Bubbles (= cell-free areas outside the scratch) are included in this area.

19

cells_covered_area_incl_bubbles_ratio [%]

68.9

0 - 100

Ratio of cell-covered area to total area of image. Bubbles (= cell-free areas outside the scratch) are included in this area.