Merging properties


I’d like to know if and how I can merge all my properties files (each one corresponding to a 96 wells plate) into a single one.
I read about MergeOutputFiles tool option (and then ExporttoDatabase tool I guess) but I also read that this does not work at the moment on Mac …which I confirm…
Apparently some people managed to use the tool on a PC but I had no such luck and I keep on having a list of errors

Is there any other way?

Thanks in advance


Hi Matteo,

Are you asking to merge the properties files into one file, or the databases that the properties files point to into one database. I suspect you want the latter…

The main question to ask is how are you storing your data? That is, in ExportToDatabase, are you specifying (1) MySQL, (2) SQLite or (3) MySQL/CSV? If (1), we have a script that I can post which will merge the databases into one, provided that the individual tables are all under the same database name. A single properties file can then be slightly modified to point at this new table.

On the other hand, if you have the individual DefaultOUT.mat files for each run, MergeOutputFiles might work, although we’d have to see what problem you are running into on the Mac.


Hi Mark,

Thanks for your answer.
Not sure how to explain myself at best so I’ll give you a simplified example:
I acquire images from plate n.1 with my first 96 samples this week and I analyze data with my pipeline. This gives me my Default.OUT file which I export to a Database using SQLite and I also ask to generate a properties file for Analyst.
Next week a plate n.2 will be ready with the next 96 samples and I will do exactly the same thing and so on each week.

So after a few weeks I have let’s say 10 folders each one with its own Default.OUT and database and properties file. Now if I want to run an analysis on ALL my samples like this, I have to analyze 96 by 96 and instead what I’d like to do is to analyze all 960 in one shot…

So I THINK by best answer to your question is: I want to MergeOutputFiles, and on the resulting merged output I use the ExportToDatabase to generate one big database and the associated properties file which now contains data from all plates…but if you have a better suggestion I’m all ears!

Now the problem is that on Mac I open the MergeOutputFiles Data Tool, I get to the window when CP asks me to choose a name and location for the resulting file but when I click on Add to add all my DefaultOUT files NOTHING happens…it’s like clicking a dead button. I read on this forum that others had the same issue but apparently someone made it using a PC…so that’s what I did and I DO get to choose my Default.OUT files to merge but when I click on Merge (or execute…can’t remember) I get an error message…which I can try to reproduce and copy/paste if it may help but ideally I’d like to use my Mac to do this 'cause it can process data faster than the PC we have…

I have the most updated versions of both CP and CPA


ANY hint?

Thanks for the clarification. MergeOutputFiles is not in a very usable state currently, unfortunately (see below). I think you’re best bet is to run your analysis pipeline on all 96 folders at once, and generate the final database that way.

Problems with MergeOutputData on the Mac is a known issue which we have yet to resolve. If you can cut/paste the error message on the PC, that would be helpful; we have an outstanding bug report for which we are awaiting a data set to reproduce it.