How to guide: Annotation tool (ROI)

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 ...