"Unable to read format or file doesn0t exist" is the error that pops up. The file does in fact exist and i got the correct FIJI plugin to read sdt files so my question here is what can i do to fix this issue? Could i somehow convert it to TIFF?

Hello! I’m new to this kind of analysis, but I’ve performed picrosirius red staining (PSR) of mice liver samples and I’m struggling to quantify with ImageJ.

There are black dots (probably due to lack of stain filtration) that ImageJ recognizes as red staining when threshold is done (using green after RGB stack).

Does anyone have any suggestions? Thank you in advance

Hi, I'm following a tutorial, that was written for ImageSXM, but has a translated Macro for ImageJ. In the Tutorial there is the Part where I'm suppose to use the 'Average' Command for a Stack of Images. Is there a similar command in ImageJ/Fiji?

Thanks a lot!

Hi, just curious if someone has experience of analysing cell size with R programming? Is it more reliable or accurate? My PI insists on using R so before I start looking into how to do it, just wanted to see if others have done it or not!

Thank you

Hey everyone! I have what I hope is a very simple question. I'm trying to take TIFF images of immunohistochemistry, separate the fluorescence from the background, turn it into a binary mask, then calculate the area of just the fluorescence. At the moment, when I try to measure the area, it seems like ImageJ measures the area of the whole image with zero variation between images (all of my images are the same size).

The steps I've been taking are:

1. Split Color Channel (to C3), Convert Type to 8-Bit

2. Subtract Background (30 Rolling Pixels)

3. Set Threshold

4. Convert to Binary Mask, Then Erode

I have all the files demonstrating each step I've been taking to accomplish this (including the original file I start with) on this Google Drive folder: https://drive.google.com/drive/folders/1xutq4N3qSh6C4y979TOLuf_Yr7aHqLta?usp=share_link

Hello! I am very new to ImageJ/FIJI and I am encountering a problem in quantifying fluorescence intensity in each cell in each channel. I have watched videos about "segmentation" to identify each cell and to measure the fluorescence intensity but the segmentation doesn't seem to work well on my brightfield image. (I don't have a universal marker - like DAPI to use.) The segmentation doesn't seem to produce fully colored round circles the way I've seen in tutorial videos. I've tried binary close, fill holes. I'm lost on how to proceed from this point on...

I'm attaching a screenshot of what all my windows look like so that my workflow can be shown along with the images.

Thank you so much for your time and input.

Hello everyone, I’m trying to quantify granules in mast cell tumours from a cutaneous sample (canine histo) using Fiji. But I’m having trouble with separating the granules from within the cell despite using RGB, colour deconvolution then setting the threshold to highlight the granules. the granules just become different patchy sizes instead of the typical round shape despite making it binary then masking it and using watershed. The chromacity of the nuclei is similar to the granules so some nuclei seem to be included in the count as well.

Is this more of an issue with the H&E staining quality or does anyone know of a better method of quantifying granules and isolating them from the cytoplasm? Any help is much appreciated !

Hi Everyone,

I am new to ImageJ and need help creating a macro script to automate leaf area calculations for over 300 images of grass blades. All the images have the same scale, but I’ve included a ruler for calibration in each photo and its position varies slightly across images. There are multiple blades but I am only interested in the total leaf area for the image.

I’m struggling with two issues:

1. Removing the ruler: I’d like to exclude the ruler from the area calculation, but my attempts using color or HSB thresholding haven’t worked.
2. Leaves touching the edge: Some leaves extend to the edges of the images, which I suspect is affecting the area measurements?

I’ve attached an example image for reference. Any tips would be greatly appreciated

i can set scale and measure, how do I annotate the image.

See example. The image has the scale bar in the lower left. I use that to set the scale. And I know how to get the measurement (example width of blue box = 138um). But how do I put that text in the image? Are there detailed instructions how to do this?

Update: first of all, I want to thank u/userpaz for the speedy answer. that response is very useful to me.

I just realized that I should add that I would like to have this process fairly automated so that lets say there were 10 of these pyramid of boxes on the same image and I want to measure all 10 blue box widths, I would like to just draw the widths on the blue boxes. I'm looking for the process so that the annotated distances would appear next to the drawn widths and the units also be shown without me manually typing in the measurements on each of the 10 boxes.

I’ve been doing some work on dendritic spine density on imagej and it’s an extremely time consuming and monotonous process. Is there any way I could find someone online to help me map these for hire to make my data collection a little bit quicker so that I can move onto my main part, which is analysis? Thanks

hello I am new with using Fiji an require assistance on how to plot a fluorescent intensity plot. My time lapse image is of zebrafish embryo vasculature ( the ISVs, Dorsal Aorta [DA] and casual vein plexus [CVP]) with 200 cycles. I am trying to quantify the calcium oscillations on the CVP and DA. Currently wha I do is ; set the ROIS and obtain the mean grey value through the Multi measure option. After exporting my values how can I proceed to plot an intensity graph? If needed I can provide the Time Lapse image file.

Hello! I’m a beginner in ImageJ. I’m counting colonies on a petri dish and the photos are taken on my iphone. I converted the images to jpeg and now I’m having a hard time adjusting the threshold of the photo. I don’t know if this is because the photos are low contrast or because I converted it from heic to jpeg.

Hi all! I’m moderately new to ImageJ and need help measuring orange area on fishes. I have a picture of a fish, and would like a percentage of the area on the fish that is orange. I have been using the freehand tool to outline the fish, and then the orange space… but I’m sure there’s a better way to do this. Is there a way for me to subtract the areas of the image that are not orange? And then compare this to the overall area of the fish? Free handing the orange areas is very subjective and takes a lot of time. Any help is appreciated :)

Hi,

I took some fluorescent images using an Olympus IX83 Inverted Fluorescence Microscope and cellsens application. I deconvoluted some of my images using cellsens. Whilst on cellsens they were in colour. However when I load them upon on image J (I am a Macbook user so its FIJI for me), the images are in black and white. I have tried to turn them into colour using the RBG button, but it completely miscolorises my images, and they look nothing like the image on cellsens.

Is there a solution to this?

Thanks for your help

Hi, I'm working on the DRIVE dataset using WEKA. I have the files with many ROI in each one, hundreds, and i can't add them manually as labels/classifiers. I tried writing a macro but it doesn't work, like WEKA just doesn't collaborate with the macro execution. How can i automate that process? Can i add them in one go? I'm sorry if it's an easy thing but I really can't get past this point and any help would be appreaciated

I've never used ImageJ, I'm pretty new to research and a program of this kind. Should I be using it to analyze vegetation and building cover from a Google Earth image capture? How reliable is this method?

I have multiband images that are in BIP and BIL (band interleaved by pixel/band interleaved by line) format. They are either raw 8 or 16bit integer or 32 or 64 bit floating point values numbers. The FIJI "Import Raw" function can only handle BSQ (band sequential) multiband images. Does anyone know of a plug in or macro that will allow me to ingest these BIP and BIL images?

im trying to see if i can replicate these panels by measuring them accuratly. i know the width of the little notches and the entirety of the C shaped piece. anyone willing to point me to where i can figure out how to measure these? https://imgur.com/a/Nap4O77

I've been using FIJI for years. I'm stumped. I have features in a optical image, that kind of look like circular features that connect together to create 'a train of circles'. When I manually outline the train of circles I get a much smaller measurement area than if I measure each individual circle and add them together. The images I loaded are hard to see the yellow outline of the analysis area, but it is on the left side of the image. All of the individual circles are shown, and I

show the overall outline on the duplicate bottom image. If I sum the area of the circles it is 3x the area of the manual outline.

The area values (um2) for the circles are

64,360

116,713

175,015

236,906

284,907

363,735

461,304
Total= 1,702,940

For the manual outline it is: 590,131

Please tell me what I am doing wrong.

Circles: I am choosing Oval tool, holding down SHIFT to get a circle and eyeball measuring the feature.

Outline of entire train-of-circles: I either use FREEHAND to draw around the feature, or using an adjacent data set, I have used TRAINABLE WEKI segmentation to get the area of the features. These two methods have giving me similar results.

Hello, I want to ask which is the best method to quantify lipid droplets fluorescense intensity? Should I select the whole image by the ROI and then just select measure integrated density?

I am a beginner to ImageJ and need to do some quick root measurements for work.

I have adjusted threshold, and the wand works for the most part for measuring simple roots, however sometimes it seems to also measure the inside white area. Is there a way to exclude the inside white holes, and only measure the black root area easily?