ROI: Folders - Requirements - Data Analysis

gusferguson commented 8 years ago

Note: Discussion on naming - Folders vs, Containers vs, something else is on-going. “Containers” is used in this document without prejudice.

From Michael Porter 27/11/2015

Context: Microscopy Image Data or HCS Data ROI Generation: drawn in UI or drawn by script/3rd party software

ROI container would be used to identify a selection of ROIs that analysis would be run on.

different sets of ROIs would be on single or across multiple images/datasets/projects
currently have to draw ROIs - do analysis - delete ROIs - draw new set - do analysis and so on
have to redraw ROIs set to repeat analysis
being able to group ROIs in container would allow repeated and/or serried analysis

Need to be able to:

add ROIs to container at time of drawing
select ROis and add to existing/newly created container
create container - select ROIs to add to it

Only need containers at ROI level - not at shape level.

Visualisation of Structure:

roi containers 1

sbesson commented 8 years ago

Thanks @gusferguson, a related Data Analysis use case I can think of is the case where the data analysis will generate ROIs (typically image segmentation but you can also think about object detection...). Having the ability to group regions of interest generated by analysis would allow one to store multiple analysis runs (with different parameters, algorithms....).

stelfrich commented 8 years ago

Having the ability to group regions of interest generated by analysis would allow one to store multiple analysis runs (with different parameters, algorithms....).

Another (to me obvious) use case for grouping is that ROIs are semantically connected, i.e. they share common characteristics. I am thinking about intracellular ROIs that are in groups according to the cells they have been detected in.

will-moore commented 8 years ago

In this use case, you are not using folders as a primary way of finding ROIs: Merely as a way of filtering ROIs within Images that you've identified by Dataset/Tags, right? So you only need to see ROI folders once you've loaded the image & ROIs.

stelfrich commented 8 years ago

Merely as a way of filtering ROIs within Images that you've identified by Dataset/Tags, right?

Right.

So you only need to see ROI folders once you've loaded the image & ROIs.

Maybe I haven't thought it through completely, but yes.

ome / design

ROI: Folders - Requirements - Data Analysis #2