Multichannel intensity

PaulSheppard

I have a multichannel fluorescence image. Want to segment the nuclei (blue DAPI channel). Then I want to measure the intensity in the other channels (e.g. FITC, Texas Red) 'under' each of the nuclei. Then make a table with the intensity of each channel for each nucleus. I think this should be simple but I can't work it out.

YuriG

Hi Paul,

It's not really straight forward as every channel is represented by different image. One solution could be to
1. create measurements outlines on one channel (DAPI),
2. collect intensity measurements to Data Collector.
3. Copy measurement outlines to Features Manager
4. Switch to another channel, set measurement outlines from Features Manager, collect data to Data Collector.
5. Repeat step 4 for all channels (FITC, Texas Red)

Another solution is to use Intensity Tracking functionality, which provides intensity measurements for all channels in one table, but it will work only if your image set has more than one Z-position or time point. In that case you can create outlines as described in Steps 1 and 3 and then activate Intensity Tracking view and copy the outlines from Features manager as "Intensity tracks" to the composite image. Intensity measurements from all channels will be reported in the tracking table:



Yuri

YuriG

Features Manager you can open from the Selection tab, Features group, Features Manager button. When you open Features Manager panel you will see controls to add and set features from/to active image.

Yuri

JeffK

Hi Paul,  You will need to use the Parent/Child App, which will cover this type of analysis.  We have a new one that I will post in the next day or so.  

PaulSheppard

Thanks to Yuri and Jeff. I'll have a go - look forward to receiving the parent/child app.

PaulSheppard

I've fallen over on point 1. See attached screen shot.
I draw my measurement  polygon, when I double click to close the shape it disappears. I can see that a measurement is made in the data table but can't see the outline on the image. Tried toggling the light bulb but makes no difference. Must be doing something stupid.


een shot. 

YuriG

Paul,

I see that you have activated Intensity tracking, it will work only for multi-frame images. Switch it off and try again.

Yuri

PaulSheppard

'Reset measurement options' - fixed it.
Now I am stuck on point 4 'set measurement outlines from Features Manage' - where do I find this?

PaulSheppard

OK thanks