1.0.0 Cytosolic and Nuclear Translocation Application Documentation
- polina.vinogradova (Unlicensed)
- Philipp Kainz
- Michael Mayrhofer-Reinhartshuber (Unlicensed)
Application Name | Cytosolic and Nuclear Translocation |
|---|---|
Version | 1.0.0 |
Documentation Version | 01.06.2021 - 1 |
Input Image(s) | 2D (standard and/or WSI) / Time Series Images; Grayscale, (8/16 bit) |
Input Parameter(s) | Regions of interest (optional) |
Keywords | gene regulation, signal transduction, protein expression, HEK, RBL, EAHY, fluorescence, in-vitro, single cell analysis, live cell imaging, microscopy, transcription factor, nuclear import |
Short Description | Measurement of intensity and intensity ratios of fluorescence protein expression in the nucleus and cytosol of detected cells imaged by fluorescence microscopy. |
References / Literature | For more information regarding the assay check e.g. https://www.mdpi.com/1422-0067/21/12/4410; Reference laboratory: Medical University of Graz, Biophysics: Klaus Groschner, Rainer Schindl |
Table of contents
IKOSA Prisma Cytosolic and Nuclear Translocation
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@ikosa.ai.
Application description
This application automatically detects cells in fluorescent microscopy images that are used during research of gene regulation and signal transduction. For each cell, heterologous fluorescence protein expression is automatically measured by measuring cytosol and nucleus intensity and calculating intensity ratios (intensity cytosol/intensity nucleus). The application was developed and tested with images showing HEK, RBL, and EAHY cells. This analysis can also be performed on time-lapse recordings (Time Series) uploaded as 8 or 16-bit multipage TIFF files.
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 (standard and/or WSI) or Time series
Check image formats | 1 (Grayscale) | 8 Bit or 16 Bit | WSI formats: arbitrary Standard images: max. 25,000 x 25,000 | 0.15 - 0.25 |
Image content Fluorescent microscopy image showing (single) HEK, RBL, or EAHY cells, typically taken with 40x or 20x magnification. Additional requirements None. | ||||
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 overall analysis results for the input image or all inclusion ROIs. |
| 2 | csv | results_01_cells.csv A csv file containing the analysis results for all detected cells in the input image or inclusion ROIs. |
| 3 | jpg | results_vis/vis.jpg (2D image, no ROI), or results_vis/t<time-step>.jpg (time step <time-step> of time series, no ROI), or results_vis/<roi-id>.jpg (2D image, ROI <roi-id>), or results_vis/t<time-step>_<roi-id>.jpg (time step <time-step> of time series, ROI <roi-id>): A visualization of the analysis result for a specific time step for either the whole image (if no inclusion ROIs selected for analysis) or each individual inclusion ROI. Each visualization includes two parts:
 |
| 4 | json | roiMeta.json A json file containing all information regarding the ROIs defined for the analysis job to ensure reproducibility. Please note: The file is empty if no ROIs were defined for analysis. |
| 5 | jpg | rois_visualization.jpg or t<time-step>_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. Please note: This file is only created if inclusion ROIs were defined for analysis. |
| 6 | json | jobResultBundleMeta.json A json file containing all information regarding the analysis job (application name and version, project, etc.) to ensure reproducibility. |
Content
results.csv
Single csv-file
If one or more time steps (of a Time Series) were specified, the results in a specific row refer to the time step 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 | 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. |
3 | roi_name | “central” | text | Custom text to identify the ROI. Empty, if no inclusion ROI is specified and the whole image was analyzed. |
4 | total_nr_of_cells | 3 | 0 - | Total number of detected cells. |
5 | nr_active | 1 | 0 - | Number of active cells (nucleus detected that has higher intensity than cytosol). |
6 | nr_inactive | 1 | 0 - | Number of inactive cells (nucleus detected that has lower intensity than cytosol). |
7 | nr_homogeneous | 1 | 0 - | Number of homogeneous cells (no nucleus detected in cytosol). |
results_01_cells.csv
Single csv-file
If one or more time steps (of a Time Series) were specified, the results in a specific row refer to the time step 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 first 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 | 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. |
3 | roi_name | “central” | text | Custom text to identify the ROI. Empty if no inclusion ROI is specified and the whole image was analyzed. |
4 | object_id | 5 | 1 - | ID of the cell corresponding to id in visualization of ROI or image. |
5 | I_bckg | 229.1 | 0 - | Image background intensity (determined as minimum intensity). |
6 | I_cyt | 479.7 | 0 - | Cytosol(es) area mean intensity. |
7 | I_nuc | 411.8 | 0 - | Nucleus area mean intensity. |
8 | I_cytbckg | 250.7 | 0 - | Cytosol(es) area mean intensity with subtracted background intensity (I_cyt - I_bckg). |
9 | I_nucbckg | 182.8 | 0 - | Nucleus area mean intensity with subtracted background intensity (I_nuc - I_bckg). |
10 | R_nuc_cyt | 0.73 | 0 - | Ratio between nucleus and cytosol mean intensity with subtracted background intensity (I_nucbckg / I_cytbckg). If the cell is homogeneous (no nucleus), R_nuc_cyt is set to 1. |
11 | is_active | 1 | 1 / 0 | Boolean indicator if the cell is active (I_nuc > I_cyt). |
12 | is_inactive | 0 | 1 / 0 | Boolean indicator if the cell is inactive (I_nuc < I_cyt). |
13 | is_homogeneous | 0 | 1 / 0 | Boolean indicator if the cell is homogeneous. “1” if no nucleus area is detected. |
Error information
More information about errors can be found in the Application Error Documentation.
Contact
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