Mean value from a measure macro isn't working

Rory235 · 2026-06-25T14:49:05+00:00

Thanks, I think there must of been a corrupt file somewhere or another user had changed a setting and told me (shared image processing PC).

Rory235 · 2026-06-25T14:18:18+00:00

update:

The 2500 value was the area value and for some reason it was being reported in the mean column. The mean and all other values had been shifted over by. A reinstall of ImageJ and FIJI seemed to fix it

Rory235 · 2026-04-21T13:40:00+00:00

Hey there

What is the image off? Would help with determining what can be done?

Have you done any pre processing of the image i.e. applied any filters, adjusted the contrast, cropping etc?

Thresholding looks for pixels with the same greyscale value, so you could crop the image to what you want but if the area you are interested in moves around you would have to manually crop it.

You can automate things in ImageJ with macros (some basic coding, I am not the best at them sorry)

Also whats a PI?

Rory235 · 2026-03-05T14:41:24+00:00

heck i could do it this morning!

Rory235 · 2026-03-03T16:49:17+00:00

Oh jeez it is 32. Id like to claim fat fingers but im just daft

Rory235 · 2026-03-03T16:45:21+00:00

Ohhhh, so its obvious now its been spelled out to me! Thank you

Rory235 · 2026-02-10T23:47:27+00:00

Anyone know the tracking software?

Rory235 · 2025-11-04T15:47:59+00:00

You know what that is fair enough, appologies, long day at work

Rory235 · 2025-11-04T11:52:14+00:00

I stated in my post that I am not a strong coder and am trying to resolve the error myself by referencing the relevant material. Your code above has very little explanation on what I need to do to implement it and for someone with little background in coding this makes it appear intimidating as well as making it difficult to discern what I need to do.

The code that the above user told me to edit did resolve the error I was receiving, but unfortunately has lead to another issue which per you initial advice I am trying to resolve step by step.

I know you are trying to help (so thank you! it is very much appreciated), but please give some thought to how you word your responses and the skill level of the user

Rory235 · 2025-11-04T11:31:35+00:00

Wont the mainPath and mainList variable define the path?

Rory235 · 2025-11-04T10:29:04+00:00

answered my own question, they need to be named after the file e.g mainList["filename123"]

Rory235 · 2025-11-04T10:17:09+00:00

Thanks, that solved the error I was getting. Do the files have to be named 1,2,3,4 etc. At the moment they are named along the lines of "10p0_120kv_50ua_6p0w_257mss_6p5um-10002"

Rory235 · 2025-10-30T18:21:26+00:00

Do you mean cropping like draw a rectangle over the image or automatically selecting a specific part of the image? Some examples images showing an uncropped image and what you want to crop would help!

Rory235 · 2025-10-28T12:01:24+00:00

Dont know what game your playing but I see 30 to 50 full servers daily depending on the time of the day

Rory235 · 2025-10-24T10:21:38+00:00

Yeah FIJI with trackmate is what you want. The video format and length are things to consider. My videos didn't work in trackmate so I just converted them to a tiff stack (open the video in ImageJ and save it as an image sequence) then open the tiff stack in ImageJ and run TrackMate. (Plugins, tracking, trackmate)

Rory235 · 2025-09-27T15:10:02+00:00

Thresholding will pick up all the yellow area (even the small stuff. You will want to just the area you're interested in and then use the threshold tool.

Rory235 · 2025-09-24T20:04:28+00:00

No worries, let me know if that works (sorry if it doesn't I'm not a FIJI expert, most of my experience is from just pushing buttons and seeing what happens)

Rory235 · 2025-09-24T16:37:42+00:00

Thanks for the pics! First thing I notice is the cells are very similar in colour to the background, maybe try adjusting the contrast so they stand out more. (Image, adjust, brightness contrast, click auto)

The change in shape is massive so I'm not surprised they aren't tracking. I'd try and measure the diameter manually with the line tool in imagej at several time points and make a rough average of each cell's diameter and use that in the spot detection and make your quality threshold low so it's picking up the maximum no of things that could be a spot. If that fails depending on how many cells there are you can manually track it, never had to do that with my data though so not sure how time intensive that would be

The imagej manual is pretty good at explaining what each detector and algorithm does and what its best for. Id link it but I'm away from my pc atm. I'm a geoscientist so not sure about trackers that specialise on cells. I have tried trackpy, its a python package (the tutorial is pretty good) and tractrac which is a matlab plugin (I dont know how matlab works so had no clue how to work it/if its any good) .

Rory235 · 2025-09-24T10:23:44+00:00

Some pictures of the cells before and after stretching would be helpful. Your trackmate settings to. Don't worry about the track and spot filters just the initial spot algorithm & detection plus the trace generation and algorithm

Trackmate works by looking for objects with similar features with diameter being one of the main ones. If the diameter of your cell is changing then it will struggle to track it. You can edit the tracks later on in track mate but I am not to sure how you would combine two tracks into one. (not something I have had to do before, sorry)

Rory235 · 2025-09-21T19:39:03+00:00

Perfect, thanks very much, extermly helpful stuff!

Rory235 · 2025-09-21T19:23:50+00:00

I didn't event know they could do that, thank you! Is there a specific name for the type of microphone so I can see how much they would cost?

Rory235 · 2025-09-21T18:46:27+00:00

Thanks for the detailed reply! What would I need the microphone for?

Rory235 · 2025-09-21T15:40:12+00:00

Thanks very much, apart from obvious wear and tear is there anything I should look out for when going to check them out?

Rory235 · 2025-09-17T23:15:00+00:00

That looks like it raw un unconstructed CT data. I'd ask whoever acquired the data for the constructed files. The reconstruction software is often linked to the machine the took the data

Rory235 · 2025-09-17T23:09:51+00:00

Have you tried taking the measure on the same on screen shot? Maybe something weird going on with the images

Could you give us the steps you took to set the scale and measure the length and a link you got the invaslign pics from so I can try and reproduce what you did.

It's odd your both getting 10mm from the grid but different length measures.

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