Green boxes indicate regular CellProfiler modules that were kept unchanged. Certain operations (such as Crop in this example) are not currently compatible with BisQue and are ignored without affecting the rest of the pipeline. The next three steps in the pipeline are shown in transparent color to indicate that they were inactivated.
These pipeline conversions happen automatically when the pipeline is uploaded into BisQue. For example, the first box ( BisQueLoadImages) is shown in blue to indicate that the original module(s) from the pipeline have been replaced with a BisQue specific component that allows to read images directly from BisQue. Note that some boxes have different colors. Configurations for Images, Datasets, and ResourcesĮach box represents one CellProfiler module and the arrows indicate the pipeline flow through the modules.f -l : If you aren't grouping, or simply don't want to break your data that way, you can tell CellProfiler the first and last image set number to process - i.e., to run image sets 1-5 you'd add -f 1 -l 5 to your command Put it all together:Ĭellprofiler -c -r -p /path/to/pipeline/file.cppipe -o /path/where/the/output/goes -i /path/with/input/files -g Well=A01 How can I learn more?įor a deeper exploration of all CellProfiler command line flags, please check out our much more detailed page on CellProfiler’s Github wiki: Adapting CellProfiler to a LIMS environment.įor a video demonstration, check out our YouTube video on the topic.įor running CellProfiler remotely on Amazon Web Services, check out our Distributed-CellProfiler repository as well as the video link above. g : If the "Groups" module of your pipeline is turned on, you can use the grouping variables specified there to set which group this copy of CellProfiler should process - i.e., if your pipeline is set up to group by Well, you might use -g Well=A01
CELLPROFILER PIPELINE EXECUTOR KNIME WINDOWS
If you want to break your CellProfiler job up (to run in stages, or across many machines, or many terminal windows on the same machine), you may want to add a grouping component to your command. file-list : A list of files, one per line, that should be loaded by the Images module and then analyzed by CellProfiler. data-file : A CSV designed to work with the LoadData module (See module help for more details). Unless using a batch file, CellProfiler will additionally scan all the files in this folder and try to make them into image sets for your pipeline - great if you don't want to otherwise specify input sets with one of the methods below, but be warned it can be very slow if you point it at a huge directory! i : Specifies the Default Input Directory (if any modules in your pipeline are using files you've told it will be in the Default Input Directory). Your input component can be one of a few different things - or might be omitted entirely, if you're using a batch file. p : Your pipeline file (or batch file created with the CreateBatchFiles module) you want to execute See Adapting CellProfiler to a LIMS environment for more information. c -r : Flags you need to use to run CellProfiler headless. You can drag and drop the executable into your terminal window, which is typically easier than typing it out.
CELLPROFILER PIPELINE EXECUTOR KNIME PC
If NOT, this needs to be the path to your existing CellProfiler executable, which for a PC will look something like C:\Users\UserName\ProgramFiles\CellProfiler\CellProfiler.exe , and for a Mac will look something like /Applications/CellProfiler/Contents/MacOS/cp . ComponentsĬellprofiler -c -r -p /path/to/pipeline/file.cppipe -o /path/where/the/output/goesĬellprofiler : If you've installed CellProfiler from source, rather than downloading it prebuilt from our website, just typing cellprofiler is how you'll call it from the terminal. If you're willing to script some ways to scatter the CellProfiler jobs, though, or don't mind running one job at a time, headless processing can be incredibly helpful!Ī general CellProfiler headless command will have a few common pieces, and a few that will change depending on your exact setup. It also has a major potential disadvantage in that while CellProfiler running graphically on your desktop will automatically use as many cores on your computer as you permit, CellProfiler running headlessly from the command line will only run one job at a time. Running CellProfiler from the command line has a major advantage - you don't need to spend computational power or memory creating the graphical user interface (GUI) that you're used to using in CellProfiler! Cross posted from our GitHub wiki - check there for any future updates!
0 kommentar(er)
