- #Colocalization imagej how to
- #Colocalization imagej archive
- #Colocalization imagej software
- #Colocalization imagej free
Original Data and Colocalized Data were zprojected using PowerMean (p=2) for the Red, Green, and Blue channels, and the RG2B Colocalization was zprojected with PowerMean (p=2) for the Red and Green channels, and Maximum Intensity for the Blue channel. Zprojections were performed with RGB Zprojector. Images show Zprojections of the original data and data generated with the RG2B Colocalization on autoThreshold with the colocalized pixels set to the max of the red or green channel, and generating the colocalized data as an RGB image.
#Colocalization imagej how to
How to display the colocalization data in a separate window:.Which method will be employed to set the colocalized pixels:.4.1 Coloc 2 4.2 JaCoP 4.3 Colocalization Finder 5 Precautions and notes. 4 ImageJ plugins for colocalization analysis. See Category:Colocalization for pages about.
#Colocalization imagej archive
The minimum threshhold for the greenchannel (0 tio 255) This is an archive of the old MediaWiki-based ImageJ wiki.The minimum threshhold for the red channel (0 to 255).The minimum ratio cut-off for colocalization (0.0 to 1.0).Whether auto-thresholding should be applied.Generated upon completion of processing for all of the input data. The plugin operates on a previously opened image or stack of images, and
#Colocalization imagej software
OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY IN PARTICULAR, THE AUTHOR DOES NOT MAKE ANY REPRESENTATION OR WARRANTY THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. Obtaining the explicit consent of the author. Software and in all copies of the supporting documentation for such software.Īny for profit use of this software is expressly forbidden without first Without fee is hereby granted, provided that this entire notice is included inĪll copies of any software which is or includes a copy or modification of this Permission to use, copy, modify, and distribute this software for any purpose If any data was present in the Blue channel of the original image, it willĬopyright (C) 2004 CHRISTOPHER PHILIP MAUER The colocalized data can also be displayed in a separate windowĪs an 8bit or RGB image. The colocalization data can be expressed as the average, max, or min of the corresponding red and green Alternatively, the user can choose to have the threshold values determinedĪutomatically (for each slice if a stack) via the getAutoThreshold() method in the ImageProcessor Class. To alter the sensitivity of the selectionĪlgorithm, the user can specify the minimum ratio for the pixels in question, as well as the thresholdįor the red and green channels. This method of storage for the colocalization data allows for the easyĪppreciation of the presence of colocalized pixels in a sample by superimposing the colocalizationĭata without corrupting or modifying the original data.
Whether or not there is colocalization for a given pixel, and stores the result in the Blue channel This plugin takes the Red and Green channel values from an RGB image or stack of images, determines Restart ImageJ to add the "RG2B_Colocalization" command to the Plugins menu. To the plugins folder and compile it with the "Compile and Run" command. Consideration should be given to how light is handled within the microscope and to the properties of the emission filters and dichroics.Christopher Philip Mauer (cpmauer at ) Plugin auto-detects the number of channels and if it is more than one then the plugin will. For colocalization you need a color composite image containing multiple color channels (two or more). In practice it is always best to test the control slides, since the environment in vivo or in vitro differs from that used to obtain the published spectra. In general, the plugin works in two modes: particles detection (whole image or ROI) particles detection and colocalization analysis (whole image or ROI). This overlap would be a problem if the 405 and 488 nm excitation lines were used concurrently, and the two images therefore need to be obtained sequentially using each excitation line individually. The emission spectra show considerable overlap between DAPI and Alexa Fluor-488, due to the very long tail present in the DAPI emission. It appears unlikely that the 488 nm line that is optimal for Alexa Fluor-488 would excite DAPI as well. Whether both fluorophores would be excited in practice by 405 nm must be checked experimentally using the test slides with single fluorophores.
The spectra suggest that the 405 nm excitation is not optimal for exciting DAPI, and that the 405 nm source can weakly excite Alexa Fluor-488.
#Colocalization imagej free
Published spectra can be used to predict which combinations of fluorophores will be free from cross talk. The excitation and emission spectra of DAPI (4′,6-diamidino-2-phenylindole) and Alexa Fluor-488 with excitation at 405 and 488 nm.
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