-
Notifications
You must be signed in to change notification settings - Fork 0
using
Obtain from the downloads page the precompiled jar version with GUI ImageAnalysisTools_*version*.jar. Starting with version 3.4.0, FIJI or ImageJ is required to run the GUI. Place the jar in the plugins directory and restart FIJI/ImageJ. The options described below can be accessed under Plugins>Image Analysis Tools.
In the Image Analysis Tools plugin menu, you will see a number of options of tasks to run:
Batch generate maximum intensity projections
## Run MethodThis task runs a method on an image currently open in FIJI/ImageJ. If multiple image windows are open, it will run on the current image. For multidimensional processing of images, use a hyperstack.
Upon selecting this option, it will prompt you to select a parameters file, such as one generated using the set up parameters option. Note that unlike the batch processing option, there is nowhere to specify which method to run on the image, so this must be included in the parameter file itself, using the parameter method_name, which must be the name of the java class that contains the method (case-sensitive). If it is one of the built-in methods, it does not need to contain the full package name, but this is required for custom methods. Methods currently available and their names can be viewed here. The value of the method_name parameter should be the name of one of these classes (which is the same as the filename without the .java). For more information on the parameter files, see XML Parameter Files.
Any quantification will be ignored in this task, but if there is an output image, it will be displayed after the method finished in another image window. (It will not automatically be saved to disk.)
##Process Images In BatchThis task allows you to run an existing analysis method on a single image or directory of images.
After selecting this task, a new window will open showing a number of options as well as a large text area on the right hand side where the progress of the analysis, any information, and any errors will be logged.
Three things are required to run the analysis: a method, a parameter file, and an image file or directory.
Select a method from the drop down box, or to specify one not listed choose "Custom Method" and enter its name in the box (note that this must be the full name, case-sensitive, including the full java package name for the method to run).
To select a parameter file, either type the full path to the file in the box, or use the browse button to navigate to the file. More information about the content of the parameter file, how to create them, and examples can be found on the XML Parameter Files page.
To select a file or directory, either type its full path in the box or use the browse button to navigate there. Note that the browse box can be used for selecting either files or directories; to select a directory, single click on that directory and click the choose button rather than double-clicking or entering that directory in the file chooser.
For reading images, the program uses the open-source bio-formats library http://www.loci.wisc.edu/software/bio-formats, and any image file format that can be read by this library can be used.
If the method you are using processes multiple color channels, and these are not all stored in the same file (with the exception of formats that store in multiple files but have some sort of metadata file that specifies where each color is), then you will need to follow the naming convention that the different channels of the same image must have the exact same filename except for an identifier of the color channel. These channel identifiers must be specified in the parameter file. (See the XML Parameter Files page for more information on how to do this.)
You can optionally also connect to an OMERO server to process images stored there. To use this option, select "Use OMERO server" and click the "Browse OMERO" button to connect and select the images to process (you can process either individual images or an entire dataset).
Selecting "Summarize data only" will cause the analysis not to run but will recreate the data summary from existing analysis output in case this file was lost.
###Analysis Output Formats
Analysis methods can generate both quantitative numerical output as well as image output.
The format of the numerical output varies depending on the analysis method being run, but will consist of a matrix of numbers that is output to a text file, one matrix row per line of the file, columns space separated. Numerical output is placed in a subdirectory of the image directory called "output," in text files whose name is the image name, followed by an identifier of the analysis method, followed by .out.txt. Some methods may summarize this numerical output into a single file called "summary.txt" also in the output directory. Within this file, the meaning of each column in the output should be labeled.
The format of the image output will be an ome-tiff image or images with the same name as the numerical output text file, except ending in .out.ome.tif instead of .out.txt. (If there are multiple output images, they will end in .out.0.ome.tif, .out.1.ome.tif, etc.) The image output will be placed in a subdirectory of the image directory called "output_mask." The contents of the output images will depend on the method; typically method that segment images will produce a mask where each segmented region will be assigned a unique greylevel in the images, and the background will be assigned 0.
##Set Up ParametersThis is a graphical interface for creating the XML parameter files used for the analysis methods. For more information on the XML parameter files, see XML Parameter Files.
To begin, select a parameter file using the browse button. If the file already exists, then the current parameters will be loaded from that file. Otherwise the parameters will be written to a new file.
Select any parameters needed for your analysis from the left side and select add, or drag them, to move them to the use of parameters in use. Click on a parameter in use to adjust its value. You can move parameters in use up and down (some parameters, channel names in particular, may be order sensitive) using the corresponding buttons, and remove them from the list with the remove button.
To add a parameter not in the list, select custom parameter from the bottom, and when it is added to the parameters in use, enter the parameter name, type, and value. The name and type will be locked once you have selected a different parameter, so enter these immediately.
When you are finished, click done, and this will write parameters to the specified file. If an existing file was loaded, this will overwrite the file without asking.
Click cancel to exit without writing anything to disk.
Starting with version 4.0.0, it is possible to use this window to build a new analysis method from the graphical user interface. See creating new analysis methods at runtime for instructions.
##Generate Maximum Intensity ProjectionsThis option takes a folder of multi-z-plane images and creates maximum intensity projections from them. They are output as 16-bit tiff images in a subdirectory of the original image directory called "maxintproj". The dimensions of the output images will be the same as before in all dimensions except z, whose size will be 1. Note that if you are going to run the centromere finder on the maximum intensity projections, you need to run it on the maxintproj directory, not the original directory.
##DeschmutzerizeThis option assists in the manual review of the segmentation produced by the centromere finder. Specifically, it takes a folder of images and allows you to view each image and its associated mask, lets you specify centromeres or cell groups to remove, and then runs the quantification again for each image on only the remaining centromeres.
In the "File or Directory to Process", you can select either a single image or an entire directory of images. Note that you should select the original image/folder that you specified to run the centromere finder, not the output directory.
When you are ready to begin, press start, and for each image that will be processed, two windows will pop up-- one showing the original image, and one showing the mask. If there are any regions in the mask that you want to remove, either click on them or click and drag a box around them (the rectangular selection tool in ImageJ must be active). If the "Toggle Individual Centromere" option is selected, only the centromeres that you clicked or box will be highlighted; if "Toggle Entire Cell" is selected, all centromeres in the cell of and centromere that you click or box will be highlighted. If you make a mistake, click or box again to turn a centromere/cell off.
You can also toggle the status of all centromeres in the cell using the "Toggle All" button. (We sometimes use this to select all the actual centromeres and toggle so that we remove everything else.) If processing a 3D image, this will apply only to the centromeres in the currently visible plane (though their full 3D extent will be selected).
The windows displaying the images should behave as normal ImageJ windows, so if you need to zoom in, for instance, use the normal ImageJ zooming controls.
When all the regions you want to remove are selected in red, click "Remove Selected and Continue" to quantify the images again without the selected region and move on to the next image in the directory. The new quantification and new masks will be written to subdirectories of the old output directories called "deschmutzed".
###Citation
This software was originally developed for the papers "CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly," B Moree, CB Meyer, CJ Fuller, AF Straight. Journal of Cell Biology, 2011 (doi: 10.1083/jcb.201106079), and "Image analysis benchmarking methods for high-content screen design," CJ Fuller, AF Straight. Journal of Microscopy, 2009 (doi: 10.1111/j.1365-2818.2009.03337.x). If you use this software for academic work, please consider citing one of these papers.