Application Name | CAM Assay |
Version | 3.0.0 |
Documentation Version | 28.09.2021 - 1 |
Input Image(s) | 2D (standard and/or WSI) / Time Series / z-Stack / Multichannel Images; RGB or Grayscale (8 bit) |
Input Parameter(s) | Regions of interest (optional) |
Keywords | CAM, chorioallantoic membrane, ex-vivo, angiogenesis, chick, vessel, growth, microscopy, assay |
Short Description | Quantification of blood vessels on chick chorioallantoic membrane (CAM) assay used in ex-vivo angiogenesis research. |
References / Literature | For more information regarding the assay check e.g. https://www.ncbi.nlm.nih.gov/pubmed/19007659 |
Table of contents
IKOSA Prisma CAM 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@kmlvision.com.
Application description
This application automatically segments blood vessels in microscopy images that are taken from chick chorioallantoic membrane (CAM) Assay samples and measures their total area, length, mean thickness and the number of branching points. Vessels that are in the background (lower layers) that appear blurry in the images are not detected. This analysis can also be performed on time-lapse recordings (Time Series), z-stacks, or multichannel images, uploaded as multipage TIFF files.
In the following, the requirements for an accurate analysis are given and the output of the application is described.
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 and/or WSI), Time Series, Multichannel, Z-stack* Check image format File formats | 3 (RGB) or 1 (Gray) | 8 Bit | WSI formats: arbitrary Standard images: max. 25,000 x 25,000 | typically: 1-7 |
Image content Microscopy image of CAM Assay region. Additional requirements
| ||||
*Please note: Z-stack images cannot be uploaded into IKOSA but still can be analyzed via IKOSA Prisma API.
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.
As an optional parameter, a single or multiple regions of interest (ROIs) can be defined in which the analysis should be performed (‘inclusion ROIs’).
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 or all inclusion ROIs. |
| 2 | 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. A visualization of the detected vessels contains:
|
| 3 | json | roiMeta.json A json file containing all information regarding the ROIs defined for the analysis job to ensure reproducibility. |
| 4 | 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. Please note: This file is only created if inclusion ROIs were defined for analysis. |
| 5 | json | jobResultBundleMeta.json: A json file containing all information regarding the analysis job (application name and version, project, etc.) to ensure reproducibility. Please note: This file is only included if bundled or merged analysis jobs are downloaded. |
Please note:
In the case of inclusion ROIs that are partially outside of the image, the ROIs are cropped to the areas that lie inside the image.
In the case of inclusion ROIs that are completely outside of the image, no analysis is performed. However, they are still listed in corresponding results files.
A <roi-id> is generated automatically by the application corresponding to the creation date of a ROI. The location of a ROI within an image with its specific <roi-id> can be seen in the file “rois_visualization.jpg.” ROIs that are completely outside of the image are not shown in this file.
All visualizations are downscaled to 25 megapixels (MP), if the original image or inclusion ROI is larger than 25 MP.
Content
results.csv
Single csv-file
If one or more time steps (of a Time Series), z-layers (of a z-Stack), or channels (of a multichannel image) were specified, the results in a specific row refer to the time step/z-layer/channel specified in the corresponding column.
If one or more ROIs were specified, the results in a specific row refer to the ROI specified in the corresponding columns, otherwise (empty ROI columns) the results refer to the whole image.
Column NO. | Column name | Examples | Value range | Description |
|---|---|---|---|---|
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 | Vessels_total_area [Px^2] | 3668 | 0 - #of pixels in image | Total area covered by detected vessels in Pixel^2. |
8 | Vessels_total_length [Px] | 12092 | >=0 | Total length of all detected vessels in pixels. |
9 | Vessels_mean_thickness [Px] | 6.98 | >=0 | Mean thickness of detected vessels in pixels. |
10 | vessels_num_branching_points | 776 | >=0 | Number of detected branching points. |
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@kmlvision.com.
Feel free to book a 30-minute meeting to speak with us about IKOSA and the apps!