2.6.6 Scalebar dialog and display

[MattPankhurst]

Hi Ajay, Thank you very much for Drishti. In 2.6.6, the Scalebar dialog asks for "Number of voxels". Here (attached) I've put 1000. The Scalebar returns with 1000 um. If the voxel size does not = 1 um, either the scalebar length displayed or the units displayed cannot be correct. Should the dialog instead ask "Number of voxel units?" For example, this volume has a voxel size of 3.24 um. I would like to place a scalebar of 1 mm, but I'm not sure if the length is correct, or the units (or neither?), or maybe I'm simply not understanding something correctly. Thank you, Matt

[AjayLimaye]

Yes, that is an error. I have now fixed it. Update on CloudStor https://cloudstor.aarnet.edu.au/plus/s/ykqMmmikfXxHxKC Replace drishti.exe with the one in directory 2.7

Cheers, Ajay

On Wed, May 20, 2020 at 3:40 AM Matt Pankhurst notifications@github.com wrote:

Hi Ajay, Thank you very much for Drishti. In 2.6.6, the Scalebar dialog asks for "Number of voxels". Here (attached) I've put 1000. The Scalebar returns with 1000 um. If the voxel size does not = 1 um, either the scalebar length displayed or the units displayed cannot be correct. Should the dialog instead ask "Number of voxel units?" For example, this volume has a voxel size of 3.24 um. I would like to place a scalebar of 1 mm, but I'm not sure if the length is correct, or the units (or neither?), or maybe I'm simply not understanding something correctly. Thank you, Matt [image: image] https://user-images.githubusercontent.com/20170346/82358915-1702ef80-99ff-11ea-81b8-632c822e1ff5.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nci/drishti/issues/44, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMVVLXMVQYEAPPDXCMQZQ3RSK77JANCNFSM4NFGVJZA .

--

Ajay Limaye

VIsualization Programmer, NCI Australia http://www.nci.org.au/

The Australian National University

143 Ward Road

Acton, ACT, 2601

T: +61 2 6125 4616

Want the latest news http://nci.org.au/research-news/news/ from NCI?

Find out more about NCI: YouTube http://www.youtube.com/user/NCINationalFacility / Facebook https://www.facebook.com/NCIAustralia/ / Twitter https://twitter.com/NCInews / LinkedIn https://www.linkedin.com/company/national-computational-infrastructure/

[image: cid:image002.png@01D449EE.B750D8C0]

[MattPankhurst]

Thanks Ajay, and especially for the rapidity of the fix!

I followed your instructions and confirm that the scalebar now correctly displays in um according to the input number of voxels. I put in 100 voxels and a scalebar of 324.00 um is displayed as expected.

A follow up (please tell me if you regard this is a side/separate issue and I will start a new thread) is that what would be even better is if the user could nominate the length in units, not voxels. The reason I suggest this is illustrated below. To make a scalebar of 1000 um I first calculated the number of voxels needed. The number is 308.64197. I needed this many significant figures to produce the 1000.00 um scalebar. Using less significant figures resulted in "999.99 um", which is awkward! It's obviously a piece of cake calculation for the user, but needs a little trial and error which takes time. For that reason, it'd be nice to have it integrated into Drishti for a smoother experience.

For example, what I imagine is that the user could nominate to display a scale bar of 1000 um (no decimal places), or choose to display it as 1 mm. I think whole numbers are easier to digest at a glance. In terms of workflow, the user could open the dialog box and choose to either nominate a number of voxels (for extreme precision), or nominate a scalebar length and units to display, and Drishti would calculate how many voxels are needed according to the voxel size (to the nearest voxel perhaps as that would be fit for purpose).

Thanks again, Matt

[AjayLimaye]

Yes, agreed would be more intuitive that way. Will have a look at it. Cheers Ajay

On Wed, May 20, 2020 at 9:36 PM Matt Pankhurst notifications@github.com wrote:

Thanks Ajay, and especially for the rapidity of the fix!

I followed your instructions and confirm that the scalebar now correctly displays in um according to the input number of voxels. I put in 100 voxels and a scalebar of 324.00 um is displayed as expected.

A follow up (please tell me if you regard this is a side/separate issue and I will start a new thread) is that what would be even better is if the user could nominate the length in units, not voxels. The reason I suggest this is illustrated below. To make a scalebar of 1000 um I first calculated the number of voxels needed. The number is 308.64197. I needed this many significant figures to produce the 1000.00 um scalebar. Using less significant figures resulted in "999.99 um", which is awkward! It's obviously a piece of cake calculation for the user, but needs a little trial and error which takes time. For that reason, it'd be nice to have it integrated into Drishti for a smoother experience.

For example, what I imagine is that the user could nominate to display a scale bar of 1000 um (no decimal places), or choose to display it as 1 mm. I think whole numbers are easier to digest at a glance. In terms of workflow, the user could open the dialog box and choose to either nominate a number of voxels (for extreme precision), or nominate a scalebar length and units to display, and Drishti would calculate how many voxels are needed according to the voxel size (to the nearest voxel perhaps as that would be fit for purpose).

Thanks again, Matt [image: image] https://user-images.githubusercontent.com/20170346/82440728-bcb46e00-9a94-11ea-9fb0-76d1e8ae6dc6.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nci/drishti/issues/44#issuecomment-631419425, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMVVLX54KKHNKG6Q3JBNUDRSO6CDANCNFSM4NFGVJZA .