Application Name | Fungi REPAINT Assay |
Version | 2.0.0 |
Documentation Version | 01.02.2022 - 1 |
Input Image(s) | Single Image (standard, RGB) |
Input Parameter(s) | None |
Keywords | phenomic, fungus, fungi, spore, growth, conidium, hypha, phenotype, plate, well, multiwell, 96, photo, biolog, macro, assay, microplate |
Short Description | Quantification of fungal phenomics (conidia and hyphae coverage and radial distribution) in a 96-well Biolog microplate. |
References / Literature | For more information regarding the assay check e.g. https://www.nature.com/articles/s41396-020-0709-0 . |
Table of contents
IKOSA Prisma Fungi REPAINT Assay
You can use this or any other of our image analysis applications through your IKOSA® account. If it is not listed in the available applications, please contact your organization’s IKOSA® administrator or our team at support@kmlvision.com.
Application description
This application automatically measures the relative conidia and hyphae coverage in the 96 wells of a Biolog FF microplate. This microplate includes 95 carbon sources and water. The application was trained and evaluated on images showing different stages of conidia and hyphae of the following types of fungi: trichoderma, metarhizium robertsii, aspergillus niger, and penicillium sp.
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.
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 | 3 (RGB) | 8 Bit | Max: 7,245 x 7,245 | |
Image content Photo of standard Biolog multiwell plate with 96 wells. Additional requirements
| ||||
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 | result.csv Coverage of conidia/hyphae for each well. |
Content
result.csv
Single csv-file
Column NO. | Column name | Examples | Value range | Description |
|---|---|---|---|---|
1 | well | A01 | A01-H12 | Name of the well. |
2 | coverage conidia [%] | 25 | 0 - 100 | Percentage of the well area covered with conidia. |
3 | coverage hyphae [%] | 75 | 0 - 100 | Percentage of the well area, covered with hyphae. |
4 | mean intensity conidia [0,1] | 0.60 | 0 - 1 | Mean intensity of the area classified as conidia in the range [0,1], where 0 corresponds to a bright conidia color, and 1 corresponds to a dark conidia color. Due to different illuminations in the images, the value cannot be compared between different images. |
5-14 | radial distribution [conidia/hyphae] bin [x] [%] | 50 | 0 - 100 | The circular area of the well is divided into 5 annuli. For each annulus with index [x], the percentage of the area covered by conidia/hyphae is given. A visualization of the annuli and their indices is given shown in the image below: |
15-24 | intensity histogram conidia bin x ([a, b]) [%] | 0.3 | 0 - 100 | A histogram of the intensities of the area classified as conidia. Each bin contains the percentage of the well area classified as conidia in the intensity range [a, b]. |
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!