![]() ![]() However, I can’t get the data from the Li plots to make the representation by my own. When I obtain the results I am able to see the Li plots and the ICQ, Pearson… coeficients. I run the plugin using my two images and select a ROI that is drawn on one of the images. I am having a problem using the plugin Coloc2. Problem with Li plot using coloc2 Image Analysis saveAs("Text", outputfolder + "/" + imageName + ".txt") run("Colocalization Test", "channel_1=channel1.tif channel_2=channel2.tif roi= randomization= show_all_r_values randomize pixel=1.000 channel_2_wavelength=520 na=1.40 iterations=0 use_manual_psf psf_radius=10") SaveAs("Text", outputfolder + "/" + imageName + ".txt") Run("Coloc 2", "channel_1=channel1.tif channel_2=channel2.tif roi_or_mask= threshold_regression=Bisection psf=3 costes_randomisations=10") RoiManager("Save selected", _RootFolder + "/coloc2_output/ROIs/" + imageName + ".roi") saveAs("Text", outputfolder + "/" + imageName + "ROIcoord.txt") Adjust location of ROI to center of image RoiManager("Open",_RootFolder + "/channel1/ROIs/" + imageName + ".roi") SaveAs("Tiff", _RootFolder + "/channel2/" + "channel2.tif") Open(_RootFolder + "/channel2/cells/" + imageName + ".tif") SaveAs("Tiff", _RootFolder + "/channel1/" + "channel1.tif") Open(_RootFolder + "/channel1/cells/" + imageName + ".tif") ImageName = replace(fileName,"\\.tif$", "") List = getFileList( _RootFolder + "/channel1/cells/" ) ![]() OutputfolderROIs = _RootFolder + "/coloc2_output/ROIs" Outputfolder = _RootFolder + "/coloc2_output" Creating a directory where the files are saved Megan _RootFolder = getDirectory("Choose a Directory") In general which platform does everyone prefer for getting a Pearson’s Correlation Value? However those Pearson’s R values are slightly different from those provided by Coloc2. I also tried running in batch mode the colocalization test (which worked for my whole data set) which I have commented out below. I am not a programmer so if this is not an ideal script please let me know how it could be improved. I wanted to check to see if there was something I was missing for closing that image and being able to process larger data sets with my existing script. I noted there are recommendations on here for using a groovy script or the ImageJ Ops but am not familiar with either of these options. From googling and looking here it seems that window is troublesome and getting it to close is difficult. I could not figure out how to close that window. I assume this is due to the Coloc2 window that opens during the analysis. I first tried adding memory as the error message suggested I do. ![]() When I scaled up to a larger amount of images I got a memory error around 10 images into the analysis. I pilot tested the macro on 4 images and finally got it working properly. I have previous macros that split channels and crop images, so my new macro loads those images/corresponding ROI (& re-centers the ROI) and runs Coloc2 on them. I have been trying to create a macro for Coloc2. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |