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Questions tagged [fiji]

Fiji is just ImageJ. It is a Java-based open-source image processing program that is used extensively in scientific image analysis, particularly life sciences. This tag should be used for questions about Fiji-related programming.

Fiji is just ImageJ. It is a Java-based open-source image processing program that is used extensively in scientific multidimensional image analysis, particularly life sciences. This tag should be used for questions about ImageJ-related programming.

For questions regarding general Fiji usage as well as Fiji-specific questions, the ImageJ forum is the best place to ask.

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Draw a 3d drape over the non zero non null pixels in my 3d tif image

So I have a 3d tif pixel image and want to draw a 3d drape over the non_zero non_null pixels At first I worked in a 2d manner and passed on every slice and tried to draw a shape around and then plot them to form a 3d shape but it doesnt seem to work…
Ali_Nass
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Adjusting macro to run to 14-well plate format

I have been running a Nikon Elements job that was created by a previous member of our group. The job contains a FIJI macro that stitches together an overview scanned image at 4x and then performs a segmentation of the slide, and reregisters the…
CindyMaddera
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Finding number of ROI Groups entered into Roi-Group Table plugin

I have been using the Roi-Group Table plugin, which i have cited at the bottom of this post. I am writing a macro and need to get the number of groups that were entered into the plugin, so that I may enter them into a loop that sequentially leads…
Sharon Daniel
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ImageJ (Fiji) search directory for a given file, using python with imageJ macro

I have a python class that I want to use with an imageJ macro. The python class(below) will walk(search) a directory and look for multiple files given by the user. I need to use this logic with an ImageJ macro to walk a directory and return a list…
anonymousKoala
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remove horizontal black line in a grayscale image

I have this image that has a continuous black horizontal line, and I need to remove it as a first step in enhancing it. is there a way to remove it using imageJ/Fiji or python, such as a library or a plug in? I understand the concept of using a mask…
gin
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How to use Fiji in Gitlab CI/CD as an executable?

I am pretty new to Fiji and usage of it, so I wanted to ask on how I can utilise it in Gitlab CI/CD. I use a cython file, in which I initialize Fiji. This I convert to a C file, and then use GCC to convert to an executable in the pipeline. Further,…
Jane
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How to colour code the spatial distribution of different sized lipid droplets in a high resolution image of cells?

I have recently started volunteering at a lab and have been given this open-ended ended task. I have never done any digital image analysis before which is why I come here for assistance. In this case I have been given an image of certain cells…
dantebuppi12
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Is my representation of Mean Square Displacement good using this code?

I use TrackMate in order to get the trajectories of particles, then it generates a csv file that contains positions in X, in Y and the corresponding times for each particle. I tried calculating MSD using different approaches but the result seems odd…
Zak Ariya
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OME series: not an ome-tiff master file

I am trying to open 2 dimensional tiff files with extension ".tif", whose exact name is "IMG0014_PKMO1_4000_T0002_STAR_580.tif", with the code from tifffile import imread image = imread(path_low) It manages to do every operation after those lines,…
salomepx
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Subtraction of fluorescence from two images representing the same sample

I am an oceanographer and I have a problem in my research. I am working on the FIJI software (Image J) and I have to process many images to do some quantification. I have images of samples taken with different Fluorescence : CY3 ; TxET , and DAPI I…
ArthurCo
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Display mesh in obj file format with ImageJ

I am using Fiji-ImageJ 1.53q. I used "3D Viewer" plugin and tried to display the following simple mesh via a .obj file but I don't see any cube getting visualized. The log window just displayed the filepath and if I double click on it, it opens…
fonishormon
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Use variable in calibrate function ImageJ macro

I want to convert the grayscale values to nm (height) values using the Analyze->Calibrate function in ImageJ. I also would like to do this automatically, where the desired values are read out from the file name. So I used the macro record function…
M. Middelkamp
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FIJI/ImageJ Macro not saving every analyze particles results and summary table

I have a folder of multiple Tif images, that I wish to analyze the particles, using analyze particles function. I need one channel, with all of its z-stack slices to be analysed and saved into a folder. My problem is that only every second summary…
MM1
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Is there a way to maintain the scale bar shifting from stack to images (FIJI)

I'm working with Fiji analysing several microscopy images. I'm trying to create several panels and to save some time, I'm opening all of my images in Fiji, then combine them as a stack. I place the scale bar and I was trying to separate them again…
Inês Ventura
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ImageJ macro to run through folder, merging three images at the time, skips one image during first iteration

I am making a script to merge channels together into a 4D stack. It should take three images in a folder at a time, merge them, and save the composite image. What I don't understand is that in the first iteration, it skips the 3rd image (opening…
Joost
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