Suggestions for Measurement tool development.
Posted: Fri Jun 05, 2009 11:49 amSuggestions for Measurement tool development.
As part of discussions with Donald, I have made a mixture of comments on the measurement tool (Beta 4.0.4), including some small issues and some bigger suggestions for changes.
NB: I haven't actually used the tool "in anger" to do work, but have been thinking about the types of jobs I would have used it for in a previous life!
Any additional comments and discussions would be most welcome...
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).
As part of discussions with Donald, I have made a mixture of comments on the measurement tool (Beta 4.0.4), including some small issues and some bigger suggestions for changes.
NB: I haven't actually used the tool "in anger" to do work, but have been thinking about the types of jobs I would have used it for in a previous life!
Any additional comments and discussions would be most welcome...
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).