![]() ![]() You'll be looking for an Environment Variable called CP_JAVA_HOME, which should be pointing to the Java directory in your CellProfiler installation folder. Sometimes there's a problem during the installation process which prevents this Java platform being registered. Has Windows been told where CellProfiler's Java is?ĬellProfiler comes with it's own Java language interpreter bundled inside it. To correct this there are a number of settings we need to check. This is usually caused by CellProfiler having issues detecting it's Java environment. The message which appears is hard to catch, but should be as follows: When running the program you should see a black console window, which flashes a message very quickly before closing, then nothing else happens. ![]() ![]() CellProfiler Won't OpenĪfter you've installed CellProfiler you may find that it doesn't start. Please check out the image.sc forum or our Github issues (and submit new issues as needed) if these instructions fail to work for you. Instructions for CellProfiler 4.0 installation can be found here. You can also set this in the ExportToDatabase module, but your settings will be the same on all exported properties files, so if you want each object to have different channels, editing them afterward is the only way to do that.The instructions below apply to CellProfiler 3.1.9 and earlier versions. You can set which channels are visible (and which are not) in the properties file, which is just a text file so you can edit it in any text editor you like (though from personal experience, something like Notepad on Windows or TextEdit on Mac work best because they are less likely to introduce “helpful” paragraph changes etc than something like Word. Thank you so much for your help, I am quite lost.Īs long as you don’t need to relate the objects together, you’re doing everything exactly right and can ignore that warning! I do not now how to get CPA to show me the fluorescent channel I actually want. I cannot find any related forum topics on this issue.However, when I load the property file for object 2 for example, the image that is loaded into CPA is the first channel, when I really need the second channel. The second issue is that, for now, I am producing 3 different properties files for CPA to use (one for each object type). How can I merge different object tables but keep them distinct when I have 3 different object types? I have no idea what I am supposed to do to resolve that issue.The first issue is that I am getting an error from CellProfiler on the “Export to Database Module” that says, “You will have to merge the separate object tables in order to use CPA fully, or you will be restricted to only one object’s data at a time in CPA. My goal is to train CellProfiler Analyst on my two main object types (objects 1 and 2). I have successfully made the CellProfiler pipeline and am now trying to take advantage of CPA’s machine learning Classifier tool. My images have 3 different fluorescent channels, and each channel contains a different object type (object 1, object 2, and object 3 which are object 1’s that overlap with object 2’s). Hello, I have been trying to create a CellProfiler Analyst pipeline to automate intensity signal quantification. ![]()
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