Manual tags in data collector

josephinekalm

Hi again!

My colleague has been counting cells manually by using the Manual Tag in the Measurements ribbon and dotting out one tag on top of each cell. She has also drawn two ROI's in which she does the manual counting in. This has been done to roughly 80 images. Now we want to collect all the data and I cannot manage to get it right. 

What types do I need to add to the data collector to be able to get stats for each image for number of cells and to get the size of the ROI/ROI's? Iv'e tried all sorts of combinations and I just get the total count in all classes, or mostly, nothing at all, does the data collector not recognize manual tags? Iv'e changed the ROI to a measurement in with the features manager and added them to a separate class, but instead of getting it as a separate measurement I get it as one or two more objects, as well as getting the measurement. So when I get the total number from the measurements, the ROI is included as an object in that number.

So, I want to be able to collect the number of cells (manual tags) from each image, as well as the size of the ROI. Preferably I would like to get all data in one table to be able to export it all to excel and be able to express my results in number of cells per mm2.

Please help? <span></span>

Best Regards Josephine

YuriG

Hi Josephine,

What you need to do is Parent/Child analysis. It can be done in Premier using Measurement classes.

Here are the steps.

1. Define Parent areas as Class 1. If I understand correctly, you have parent areas as ROIs. You have to convert them to Measurements using Features Manager. Set Active Class of the Measurements (Class ribbon group) as Class 1 and then set these ROIs from Features manager to the image as Measurements.

2. Convert all Tags to Class 2 (child class must be higher than 1). You can do that by adding all tags to Features Manager, removing them from the image, activating Class 2 and adding them back to the image. (after that all your tags should belong to Class 2)

Then you can use the "Group by Parent" menu item from the Grouping drop-down of the Data Table to group objects by Parents - it will give you the number of tags per parent (per old ROI).
Then you can use "Classify by Group" to assign classes according to Parent and collect data to Data Collector, Measurements Class Stats table.

Regards,

Yuri

YuriG

Hi Josephine,

Reading your question again, I can see that you may not need parent/child analysis, but just want to get total area of ROIs and total number of tags, right? If yes, then ignore the previous answer and here is the another workflow (assuming that you have image with ROIs and manual tags):
1. Set Manual Range to 0...255 (to cover whole range), In the measuremetn options set "Preserve Existing Data". Click Count - the ROIs should be measured as objects. (you can also convert ROIs to objects using Features Manager as I described in step 1 of my previous answer).
2. Load the attached CountPerUnitArea.adoxsd to Data Collector (unzip it first).
3. Click Collect - check the data table - it will have "Count Per Unit Area" measurement that will show the number of tags per mm^2 (if image calibration is in millimeters).
 
Regards,

Yuri

YuriG

Hi Josephine,

You can set Manual threshold range clicking the Manual button on the Count/Size tab, use Mono interpretation and set 0...255 range.
Alternatively, you can convert ROIs to Manual measurements using Features Manager.

If you are going to use manual tags in future, I would recommend creating measurement outlines instead of ROIs from the beginning, so you don't have to convert them later when you measure tags density.

Regards,

Yuri

josephinekalm

Thank you so much!
Stupid question maybe, but where do I set the Manual range? 
I will try the two different options out later this afternoon once the work station is free.

Thanks again, and have a nice weekend!

Cheers/Josephine