After adjust this pipeline (in attach)for this kind of images I need to validate it. What can you advise me to do?
For example, for counting objects I will ask for some people to do it manually, and compare results.
I check the option “Discard Objects touching the border” but it looks to be counting it in the top of the image. Why?
Why the module “MeasureObjectSizeShape” and “MeasureObjectIntensity” are not exported to a csv file? In fact I cannot see all the data in the displayed window!
In the displayed window “IdentifyPrimaryObjects” there’s a table with some info; what is the “Area Covered by Objects”? Is it different from the Module “Occupied Area” right?
What measured features should I relate in order to extract info about Cell Shape?
Can I monitor Cell position variation along a sequence of images, right? How?
After validate my pipeline I need to go forward: Data Storage, Image Archiving, Analysis. I’m thinking to use CPAnalyst. I saw some of the videos, but I’ve some questions about “HOW TO START”:
a) Setup MySQL Database
This should be done on my computer or in a server (at my research center)?
I would like to learn it How to do it, as I have some basic knowledge on this and I would like to Improve it (is it a difficult or sensible step?)
In case of ask for help at the I&T department what info should I give them?
b) Manage Data (Images)
After setup MySQL database where should the images be saved and managed?
c) Run CPAnalyst
What about the properties file? I read in the tutorial that the CP Module “ExportToDatabase” will have nearly complete properties. But does this module export a properties file?
d) Data Analysis
How do I extract the most accurate values of each image for each feature? Should I use all the output data from CellProfiler and manage it with CP Analyst? I mean, we can obtain some outliers when measuring each cell feature in each image, thus we would need to “eliminate” some cells to not be considered in some feature measurement.
With Best Regards,
Pipeline4.zip (393 KB)