MOE_Golgi_Analyzer_v1

<strong>Description of the folder content :</strong> <br> 1) The macro in .ijm format.<br> Suited for analysis of 3-channel confocal fluorescence microscopy images of mammalian cells (~200*200µm). <br> Requires ImageJ v1.4 with Bio-render plugin.<br> Images should be as .nd2 format but it can easily be changed, simply search &amp; replace all occurences of ".nd2" with your format in the macro code.<br> Images should be organized with every replicate of a same test-condition in a unique folder. The macro will analyze the whole folder at once and will create a folder in it to save results. <br> 2) A folder named "example_data", it contains 3 representative images that can be used to test the macro. <br> It also contains a results folder with representative data obtained via the analysis of these representative images with the macro (see Description of the macro for description of the results obtained) ____________________________ <strong>Description of the macro :</strong> input : 3-channel image with C1 = nucleus labeling (e.g. DAPI, Hoechst, etc.) <br> C2 = signal of interest, the one you want to measure in whole cells &amp; in the region of interest <br> C3 = region of interest (ROI) (e.g. an antibody directed against a particular organelle, in our case Golgi apparatus) <br> <br> this macro will : <br> count the cells according to C1 (user input of threshold values for C1) <br> create ROI(s) according to C3 (user input of threshold values, or manual setting of each image for C3) <br> measure signal of C2 (mean min max grey values, integrated density, area) in whole cells (user input of threshold values for C2) measure signal of C2 in ROI(s) <br> save results as a .csv file <br> <br> it will also create several .png images for each analyzed one : <br> C1+nucleusROI (to assess correct cell counting) <br> C3+ROIC3 (to assess correct creation of ROI(s) from C3 signal) <br> C2 (glow LUT) + ROIC3 (to assess correct thresholding of C2 signal) <br> C2+ROIC3 <br> merge C1+C2+C3