ims files which can be further processed within the software. Imaris converts proprietary microscope image files to. The MIC has an image analysis workstation that has an installation of Imaris, a large-data optimized commercial image analysis software. Select appropriate import parameters then press OK.Ĭonvert to Imaris format and use the MIC Imaris license. Drag and drop your proprietary file onto the FIJI search bar. Image.sc is an active discussion forum where you can see if anyone has had similar issues and find potential solutions. Sometimes this approach works smoothly, and other times there may be some issues getting the import to work properly. Once your data is in FIJI, you can perform 3D visualization and processing of your images and save them in a variety of other formats (eg.tif, avi. If you drag your file onto the FIJI status bar, it will use the BioFormats library to open your images as well as display the metadata. FIJI (is just ImageJ) is a powerful open-source, free software tool that can open most proprietary file formats and is available for Mac, Linux, and Windows. However, it may not be obvious how to go about opening these files on your own computer for further visualization and analysis. It’s a good idea, if you have storage capability, to retain your image in this type of format to keep the metadata which are important for reproducibility. czi for Zeiss) that store multidimensional (x, y, z, t, channels, etc.) image data along with image metadata (microscope hardware settings like laser power, filters, voxel size) in uncompressed or lossless compressed form. Each microscope manufacturer has different proprietary file formats (ex.lif for Leica. If you need any more information, I am happy to provide it.Spending quality time inspecting your data is critical for hypothesis and analysis pipeline formation. What software packages and/or plugins have you tried?.I just want to get a bit more proficient in ImageJ before tackling other cell lines. Is there any way to automate/batch processing this? The reason is because I have a quite several images that needs to undergo the same image j processing for different cell lines. I seemed to get lost on step three, because they are three channels. My first query is that is the protocol listed above appropriate.Īre there advise to improve the protocol? Results of measured intensity of fluorescence along the drawn line Go to Analyze => "Histogram A window should appear with the graph and NOTE: Be aware on which channel you draw the line, even if both channelsĪre shown, only 1 is measured (To change channel, scroll left or right, title ofĬhannel should be displayed at top of the window,) A yellow line should appear on stacked image ![]() To measure fluorescent intensity: draw line (or other shape chosen from Window appears with Colour and possibility to tick boxes of both channels.įirst tick box of Channel 1 and click More to assign appropriate colourĬhange Colour to Composite to view stack with both colours. To question asking: Convert to multi-channelĭisplay mode: change from Composite to Colour and click OK To assign the right colour to each channel, click on "Image => “Colour” =>Ĭhange Composite to Colour. Right to switch between channels both channels are shown in the same Now both channels appear in the same window (you need to scroll left and Using ImageJ to Measure Intensity of FluorescenceĢ.Go to "Image => "Stacks => “Images to Stack” Name stack, e.g. I have been provided the following protocol: What information are you interested in getting from this image? They are breast cancer cell lines called BT549 What is the image about? Provide some background and/or a description of the image. My task is to determine if the glycosidase inhibitor treatment that I am asked to evaluate has indeed altered the cellular glycosylation by examining the lectin florescence stating of the cancer cells for those treated with my compound and compared to the untreated and the positive control (deoxynojirimycin). Scan_Plate_R_p00_0_B02f00d1.TIF is the green image Analysis goals Scan_Plate_R_p00_0_B02f00d0.TIF is blue image I have been told to use the * “scan _Plate_R…” for my analysis. Images labelled “scan _Plate_R…” split the green (lectin) and blue(DAPI, nuclear stain). Have green (lectin) and blue (DAPI, nuclear stain) overlaid (merged) Share a minimal working example of your macro code.Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox) – (make sure however that you are allowed to share the image data publicly under the conditions of this forum).
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