Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

User Story #3326 (new)

Opened 9 years ago

Last modified 4 years ago

Measurement Tool: Future changes to the measurement tool.

Reported by: jburel Owned by:
Priority: minor Milestone: Unscheduled
Component: Insight Keywords: n.a.
Cc: dzmacdonald, jamoore Story Points: n.a.
Sprint: n.a. Importance: n.a.
Total Remaining Time: n.a. Estimated Remaining Time: n.a.

Description (last modified by wmoore)

We need to have certain functions in the measurement tool:

Big Images

Measurements

  • Distance between points
  • Points to be labeled, across z, t sections.
  • Track distance between sets of points
  • Track distance z, t sections for points.
  • Calculate total distance between sets of points.

Counting

  • Points
  • Assign a point a type.
  • Count number of types
  • Count change of types over t, z sections
  • Areas
  • Assign an area a type
  • Count number of areas
  • Count size of areas, by type
  • Show changes in area by type of time

Segmentation

  • Integration of segmentation tools to generate points, areas
  • Initially only try cellprofiler, later provide interface so other tools can be used.

Analysis

  • Track points
  • User assigns class to object and the tool will analyse movement, change. The result of the analysis will be graphed, displayed in a grid which can be exported to excel.
  • Optical flow, this should be able to track the movement of the cells, (other objects) over time.
  • Change analysis, calculation of stats from the change.
  • Texture analysis
  • Simple algorithm could give a user the ability to click a few points (cells) and then let the algorithm try and pre-assign the rest of the cells.
  • Specifically for cell stage

The current UI is very rough, there will be a lot of changes occurring soon.

User Interaction

Being able to group figures(ROIShapes) together is a nice way to let the user define a relationship between the figures(ROIShapes).

Need to have a way to represent group figures as being related in the UI.

Need to add way to parse group figures to allow access to the underlying figures.

Need to add a way to set the relationship the grouping defines.

More points

From discussion on forum https://www.openmicroscopy.org.uk/community/viewtopic.php?f=4&t=11&sid=704041da7d9916033dbc087f1a058d20

Main points are

  • Need to improve handling of multiple shapes within an ROI. In most cases you only want to edit the colour, text, position etc of the whole ROI at once.
  • Various UI improvements: reducing number of tabs etc.

MeasurementTool: Analysis of Current Version and thoughts for future

This ticket is for the discussion about the Measurement tool, it's current failings and where it should maybe go in the future.

This discussion can be found on the forums here

http://openmicroscopy.org/community/viewtopic.php?f=4&t=11

Will looked has made a number of comments:

Measurement tool window is not accessible in the Window >  menubar. 

Z- slider on Graph pane acts strangely. Needs two clicks to change each Z-section. 

ROIs that only have a single shape should hide the extra ROI layer. Since many uses of the tool 
will not require more than one shape per ROI. 

In the line tool plot, need to be able to see each channel plotted independently (don’t use same pixel intenstity scale). 
May also want to compare absolute intensity between channels (as now) but this is less likely. 

When drawing a line with the annotations showing, need to make sure the numbers don’t obscure the end point
that you’re trying to position on the image. 
Would be nice to be able to configure settings so that you can turn annotations on new shapes on/off. 

It seems that the inspector cannot be used to edit ROIs, only shapes? 
It took me a while to work this out, since you can select an ROI in the manager, then go to the 
inspector tab and edit. But you are NOT editing the ROI, you are editing the last shape that
you selected. 

In Inspector tab, would be nice to have the option (in a third column?) to “apply to all”, so that
if I change the font colour, or choose “Show Annotations”, I can also choose to make the same change
to all the ROIs/shapes. So, if I was editing an ROI, I would have options for ‘apply to child shapes’,
‘apply to all ROIs’ or ‘apply to all shapes’ maybe??
If editing a ‘shape’ I would have options for ‘apply to all shapes in this ROI’ (if there were >1),
‘apply to all shapes’ etc. maybe?!?

If I have a drawing tool selected and do a single click on the image, it draws a very small line/circle etc.
This is really annoying, since it can happen when I simply want to click on the iamge to bring the 
window to the front. 
Just checked in Photoshop for similar behaviour. What they do is require for you to click and drag
before you draw any shape. This would be nice because it would stop you accidentally creating
lots of small ROIs when you’re just clicking on the image. 

Text annotations: If I have an ROI with lots of shapes, and I give a text annotation to one or two, 
then all the others have “text” displayed on them, which is annoying! They should not show anything
if I have not named them. 
Also, it seems I can apply a name to the ROI but this is not displayed on the image at-all. 
If I give a name to the ROI, it could be used as the default dispaly text for all the shapes that
I have not named (instead of “text”). 

When exporting to excell, it would be nice to have the time stamps / z-positions of the ROI shapes, 
so that I can analyse how far they are apart. 
For example, I create 2 ROI points at separate Z or T (XY too), then I merge them into a single ROI. 
Now I want to know the distance between them in um or seconds. 

In fact, in the example above, I really have a line drawn between 2 points that are not on the same plane.
Really, it would be nice to have a way to draw a line between 2 such points. 
Maybe in the line tool, you could click to start the line, then scroll to a different plane and
click again to end the line. 

With the measurement tool open, I can no-longer use the mouse-wheel to scroll through Z in the image viewer.

I think putting the “Connector” tool bar button at the far right end of the tool bar might prevent the confusion
that I had when I thought it was a line tool. It’s really different from all the other buttons which are for
drawing ROIs. 



I’m thinking that there could be more ‘styles’ of ROI creation than there are now. There’s 3 I have in mind:

1) The current shape creation, where the shape is assigned to the plane on which it is drawn. 

2) A ‘floating’ shape that is not actually attached to any particular plane. This could be represented with
a dotted scrolling line. Importantly, after drawing the shape, if you scroll through Z or T, the shape would
remain in view, and you would be able to view the intensity data/plot etc. Once you have decided where you
want to place the shape, you can then ‘fix’ it so it becomes a regular shape. 

3) An ROI that spans ALL of Z or T. Not SO sure about this one, but I can think of at least a couple of
examples where I want all of the ROIs I draw to have a shape on every Z or T plane. E.g. FRAP. So, all I have to 
do for each FRAP bleach spot is to draw the spot in one T plane, and the ROI that is created has the same shape
in every T plane. 


Need to reduce number of tabs, maybe combining Manager and Inspector. 
Somehow combine Results / Intensity View / Intensity Results View into 2 tabs? 


Treat Z and T differently, with a defined hierarcy:
ROI contains 1 or more time points, each time point cotains 1 or more Z planes. 


Bitmap masks. Just remembered that this is something we discussed once! 
E.g. Use a magic wand to select contiguous pixels that are within a certain intensity range E.g. “50”.
Then convert the selected region to a mask, and use it to query the intensity of various different channels
(could include the channel used to generate the mask, or other channels). 

Change History (2)

comment:1 Changed 8 years ago by wmoore

  • Description modified (diff)

comment:2 Changed 4 years ago by jburel

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.120251 sec.)

We're Hiring!