Navigate to the cpa_example directory and select the example.properties file. A dialog will appear asking you to select a properties file. Run the CPAnalyst file created by the install process above. This file was exported by CellProfiler’s ExportToDatabase module. It can also be used to create a MySQL database. example_SETUP.SQL - Used by CPA to create an internal database (SQLite).Note: All fields described in the sections below (after the properties file example) are required unless explicitly described as optional. Contact us on the CellProfiler forums if you need help with this. This file was exported by CellProfiler’s ExportToDatabase module. Note: CPA 2.0 is not compatible with properties files from CellProfiler Analyst version 1.0, but the two formats may be easily converted by hand. On top of that, I measure the morphological properties of the cells using the modules measure objectsizeshape, granularity and intensity and finally export all the data to a SQL database to classify the different objects by their morphology using CellProfiler Analyst. per_object.csv - Comma Separated Values file for object data.per_image.csv - Comma Separated Values file for image data.images/ - Images from the screen used in the example.MyTrainingSet.txt - Example training set file to be used in the Classifier (see section V). example.properties - Configuration file for CPA (see section III).II.C Using the example datasetĭownload the CPA example dataset from or here and unzip it to create the cpa_example directory. Run the setup.exe to create the executable and shortcuts. Open dmg file and copy CellProfiler-Analyst.app to /Applications. In the eventuality that you are a Biology student or scientists who is involved in projects that entail exploring high-dimensional imagery for various research projects, then perhaps CellProfiler Analyst could lend you a hand.All CellProfiler-Analyst releases can be found here Prerequisites CellProfiler Analyst allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Not only do they allow you examine the data from the tables, but you can also analyze relationships between objects from multiple perspectives. Afterwards, you can specify the rules used to differentiate among the objects for each of the bin.įurther noteworthy features of the application are the scatter plot, histogram and density plot, all great instruments for exploring the relationship between the objects of study. Before you can take advantage of this feature, you need to fetch the object titles and sort them manually into specific bins to form a training set. The highlight of the application stems from the Classifier function, particularly since it allows you to train the computer to easily identify the objects of interest. Comes with a classifier and various plots While the latter is designed to process images and numerical data, this utility relies on machine learning-based scoring of complex phenotypes.Īt the same time, you should know that the application mostly addresses large sets of data and thus, if you are working with a large database, you can preview and analyze it from multiple perspectives. It is necessary to mention that the application has a different approach and hence, provides distinct examination tools compared to CellProfiler. While some users might be intimidated by the minimalistic looks of the main window and it could remind you of Windows' command line console, you do not require advanced technical skills or knowing commands to operate it. A tool designed for exploring large data setsįirst off, you should make sure that you have the latest Java installed on your computer. The utility comes with numerous tools that can help scientists explore and analyze large, high-dimensional image-derived data. CellProfiler Analyst is an application designed for academic research in the field of Biology.
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