Any way to add area measurement from several bruch tool areas ?

[aliocha67]

Hi, I would like to quantify the mucus staining (AB-PAS) that appears dark purple on my tissue. So I selected all the regions where I have this dark purple staining using the brush tool, so that I can determine the total area (um2) where I have mucus. Unfortunately, it seems to me that there is no way to have all the areas sum up as a single one. Adding up all the areas manually will be very time consuming, Thanks a lot for your help !

[petebankhead]

There are a few options:

• Get the measurements from Measure → Show annotation measurements, copy them into a spreadsheet and add them up there
• When you're drawing with the Brush tool (or the Wand might be nicer, if you have good contrast between the purple stain and surroundings), hold down Shift to append to an existing annotation - if you're pressing Shift, different regions can be discontinuous but still counted as one (similarly, you can hold down Alt to use the Brush or Wand and subtract regions)
• Select all the annotations (either in the Annotations pane on the left, or by alt-clicking on them with the Move tool selected in the main image), right-click on the image and choose Annotations → Merge selected annotations

Hopefully one of those helps!

[aliocha67]

Hi Pete,

That's very helpful, thanks a lot ! It will make my analysis way faster.

Sincerely,

GOEPP Julie Manager of the Primary Airway Cell Biobank (PACB) Cystic Fibrosis Translational Research Center (CFTRc)http://mcgill.ca/cftrc/platforms/primary-airway-cell-biobank-pacb McGill University - Department of Physiology McIntyre Building, Room 1012 3655 Promenade Sir William Osler Montreal – Qc – Canada – H3G 1Y6 (514) 398-4323 (ext #2 or 3) PACB Websitehttp://mcgill.ca/cftrc/platforms/primary-airway-cell-biobank-pacb

---

De : Pete notifications@github.com Envoyé : 21 juin 2018 11:23:17 À : qupath/qupath Cc : Julie Goepp, Ms; Author Objet : Re: [qupath/qupath] Any way to add area measurement from several bruch tool areas ? (#179)

There are a few options:

• Get the measurements from Measure → Show annotation measurements, copy them into a spreadsheet and add them up there
• When you're drawing with the Brush tool (or the Wand might be nicer, if you have good contrast between the purple stain and surroundings), hold down Shift to append to an existing annotation - if you're pressing Shift, different regions can be discontinuous but still counted as one (similarly, you can hold down Alt to use the Brush or Wand and subtract regions)
• Select all the annotations (either in the Annotations pane on the left, or by alt-clicking on them with the Move tool selected in the main image), right-click on the image and choose Annotations → Merge selected annotations

Hopefully one of those helps!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/qupath/qupath/issues/179#issuecomment-399142573, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmmAR_KTr2VFQD77eEVrU9ppSThbe9tKks5t-7pkgaJpZM4UyRk4.

[aliocha67]

Hi Pete,

Now I noticed that when I have a polygon drawn and I want to select an area with the brush within the polygon, it does not let me, or it would increase the size of the polygon if the brush is used at the edges of the polygon. Is there a way to select an area with the brush, within the polygon area ?

Thanks again !

GOEPP Julie Manager of the Primary Airway Cell Biobank (PACB) Cystic Fibrosis Translational Research Center (CFTRc)http://mcgill.ca/cftrc/platforms/primary-airway-cell-biobank-pacb McGill University - Department of Physiology McIntyre Building, Room 1012 3655 Promenade Sir William Osler Montreal – Qc – Canada – H3G 1Y6 (514) 398-4323 (ext #2 or 3) PACB Websitehttp://mcgill.ca/cftrc/platforms/primary-airway-cell-biobank-pacb

---

De : Julie Goepp, Ms Envoyé : 21 juin 2018 11:43:20 À : qupath/qupath; qupath/qupath Cc : Author Objet : RE: [qupath/qupath] Any way to add area measurement from several bruch tool areas ? (#179)

Hi Pete,

That's very helpful, thanks a lot ! It will make my analysis way faster.

Sincerely,

GOEPP Julie Manager of the Primary Airway Cell Biobank (PACB) Cystic Fibrosis Translational Research Center (CFTRc)http://mcgill.ca/cftrc/platforms/primary-airway-cell-biobank-pacb McGill University - Department of Physiology McIntyre Building, Room 1012 3655 Promenade Sir William Osler Montreal – Qc – Canada – H3G 1Y6 (514) 398-4323 (ext #2 or 3) PACB Websitehttp://mcgill.ca/cftrc/platforms/primary-airway-cell-biobank-pacb

---

De : Pete notifications@github.com Envoyé : 21 juin 2018 11:23:17 À : qupath/qupath Cc : Julie Goepp, Ms; Author Objet : Re: [qupath/qupath] Any way to add area measurement from several bruch tool areas ? (#179)

There are a few options:

• Get the measurements from Measure → Show annotation measurements, copy them into a spreadsheet and add them up there
• When you're drawing with the Brush tool (or the Wand might be nicer, if you have good contrast between the purple stain and surroundings), hold down Shift to append to an existing annotation - if you're pressing Shift, different regions can be discontinuous but still counted as one (similarly, you can hold down Alt to use the Brush or Wand and subtract regions)
• Select all the annotations (either in the Annotations pane on the left, or by alt-clicking on them with the Move tool selected in the main image), right-click on the image and choose Annotations → Merge selected annotations

Hopefully one of those helps!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/qupath/qupath/issues/179#issuecomment-399142573, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmmAR_KTr2VFQD77eEVrU9ppSThbe9tKks5t-7pkgaJpZM4UyRk4.

[petebankhead]

If you zoom in more, by default the brush will be effectively smaller and so it's easier to select a region without changing the shape.

Of you change just switch to the Move tool to select another region by double-clicking on it, without any risk of changing its shape. You can toggle between tools by just pressing M and B.

In general, you might find 'locking' annotations helpful - that helps avoid changing them accidentally, and also allows you to draw new regions inside an existing annotation with the brush. To do so, select the annotation and then right-click on it, and choose Annotations → Lock.

Finally, if you are doing a lot of painstaking annotations be sure to save regularly (Ctrl + S)... or consider trying the beta/pre-release version here. Installation is a bit more awkward, but it does provide (limited) undo support along with many other improvements - so may be worth it.

[Zhengmingxia]

First, draw a rectangle

Then select the area you want within the rectangle with the “Wand” tool (it will go out of the rectangle)

Next, zoom in the image, hold down the "Alt" key and use the "Brush" tool to erase the area outside the rectangle