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Data Collector Advice
Hi! Thank you so much for all of your previous support. This one may be quick and easy if I am just not finding the correct functionality.
I have a 3 channel fluorescence image (originally CZI) that I have exported as an RGB TIF, and opened in ImagePro. I am looking for a simple measurement of the area above threshold in each channel, optimally with output being in relative percentage of each area (which may overlap, so it's really more of a "how much blue area vs red area vs green area"). Currently I can get the values I am looking for by using Count/Sizes and Summary measurements, but I would like to get that output in a single line, and was hoping Data Collector could allow me to do this.
The red circled values are the Sums of my Count/Size areas by class, classify by group, statistics per group.
I can use the data collector to get individual values for objects, or a total area sum (which is the same for all objects), but I am not sure how to get a single line per image showing the area (and/or percent area) for each class. The app you posted last time for Phase Analysis was VERY close to doing this (at least in output), but does not seem to handle RGB image thresholding. The output would then be a list of 3 or 6 values per image (one row each) for hundreds of images.
Am I going about this the wrong way? Is there an easier way than using the data collector to get single class based measurements? Or should I be looking at Excel macros for downstream data sheet manipulation?
I have a 3 channel fluorescence image (originally CZI) that I have exported as an RGB TIF, and opened in ImagePro. I am looking for a simple measurement of the area above threshold in each channel, optimally with output being in relative percentage of each area (which may overlap, so it's really more of a "how much blue area vs red area vs green area"). Currently I can get the values I am looking for by using Count/Sizes and Summary measurements, but I would like to get that output in a single line, and was hoping Data Collector could allow me to do this.
The red circled values are the Sums of my Count/Size areas by class, classify by group, statistics per group.
I can use the data collector to get individual values for objects, or a total area sum (which is the same for all objects), but I am not sure how to get a single line per image showing the area (and/or percent area) for each class. The app you posted last time for Phase Analysis was VERY close to doing this (at least in output), but does not seem to handle RGB image thresholding. The output would then be a list of 3 or 6 values per image (one row each) for hundreds of images.
Am I going about this the wrong way? Is there an easier way than using the data collector to get single class based measurements? Or should I be looking at Excel macros for downstream data sheet manipulation?
0
Best Answer
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OptionsIt is also possible to put all class stats in one row, you just have to add custom measurements moving Class stats to Measurements Stats table. I've attached the ADOXSD file, which will collect Sum of areas per class into 3 different columns, so it will look like this:
You can rename columns to match you classes.
Yuri0
Answers
Then you just collect the data and get the singe value per class.
I've also attached the Data Collector measurements file (zipped).
Regards,
Yuri
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Below has the default export from the Data Collector on the left, and the transposed (through Excel) on the right. Unfortunately each exported block would need to be handled individually to create columns with related values.
Or better yet, a header line and then one line for each image with the name and the 3 values.
Regardless, the main problem is already solved, thanks. I did not notice that I could use the "Edit" function to change the (average) to (sum) which had stumped me earlier when trying to use Class stats.