How to guide: Annotation tool (ROI)
Purpose of tool
Select regions of interest (ROIs) in images.
How to draw ROIs
To begin drawing an ROI, click on one of the three green button depending on the shape you would like to draw.
For the polygon:
Click on the image, if possible around the edge of a region that needs to be annotated. The annotator will drop a point (vertex) at that position.
Add more points by clicking all the edges of the ROI you would like to mark.
Each point can be dragged by doing a long click and moving at the same time
Doing a right click on a point will delete it
For the circle:
The first click will position the center of the circle
The second click will position the outer line of the circle
For the rectangle
The first click will position one corner of the rectangle
The second click will position the opposite corner of the rectangle
Rectangle can be dragged by doing a long click and moving at the same time
To select multiple ROIs in the same image, click on the add ROI button again and follow the same procedure as before.
Previously drawn ROIs can be edited by selecting their corresponding Edit nodes button.
An ROI can be removed by clicking on the delete icon shown next to that ROI.
Saving the results
Once the ROIs have been selected, the coordinates of the bounding regions can be saved on the cloud (CODI) or to the local computer in a JSON file by clicking on the save button on the top right of the right hand panel. Below is the JSON representation of the two ROIs shown above.
Related Articles
How to guide: Counting tool
Tool view Purpose of tool Counts the number of localisations or ‘bins’ by channel around a set of centre points - currently the centroids of a clustering result. Contents Inputs Results Outputs Inputs The centre points for counting come from a loaded ...How to guide: Clustering tool
Tool view Purpose of tool The tool performs clustering on localisation data to find biological structures and quantify their statistical and morphological properties. The default clustering method is HDBSCAN. The cluster results can then be ...How to guide: Filtering tool
Tool view Purpose of tool Enable user to filter out points based on their properties and save the output for further analysis in workflow. Contents Input parameters Multiple channels Output results Input parameters The points in dSTORM acquisitions ...How-to-guide: Temporal grouping tool
Tool view Purpose of tool In localisations-based super-resolution microscopy, each fluorescent molecule can emit ("blink") multiple times, depending on its properties and the super-resolution technique used. Those blinking events are localized ...How to guide: Visualization panel
For the moment CODI is only able to display super-resolution microscopy data, meaning images create from localizations of blinking event. For the visualisation or analysis of raw images, such as brightfield, widefield or tracking, please us NimOS or ...