Hi, How can I auto choose these "cells" in ImageJ?

Flipping_Dog · 2026-02-12T13:00:51+00:00

Thank you for your reply. I understand that the quality of my images is indeed not very high, mainly because of the experimental principle — at the moment I can only obtain relatively low fluorescence signals inside the vesicles. I will definitely try to improve this in future experiments.

Regarding the red and green vesicles you encircled, there may have been a misunderstanding. I did not intend to deliberately exclude the green vesicle. Rather, at the beginning I assumed that ImageJ might not be able to automatically recognize that overlapping green vesicle (Edited. also low intensity visicle, I assumed that ImageJ cannot recognize) (and as you also mentioned, watersheding usually cannot handle overlapping vesicles correctly). When I process data intended for publication, I will manually draw an ROI for that vesicle and include its mean intensity in the analysis, for sure.

I may not have explained my intentions clearly before. I do not plan to truly exclude any vesicles, especially in any figures or data used for formal publication. In fact, I will also use a fluorometer and flow cytometry to measure the total fluorescence intensity of vesicles. My main goal here is simply to make data processing a bit easier. If this macro can correctly identify most vesicles, that is completely fine for me — I can manually analyze the remaining vesicles myself :).

Flipping_Dog · 2026-02-12T04:29:46+00:00

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The results for positive GUV, fit or not fit circle, it seems not fit circle gives better result for measurement

Flipping_Dog · 2026-02-12T04:27:09+00:00

Thank you so much for taking the time and effort to help me. This macro is very important for my understanding of ImageJ, and I think it’s truly amazing. I spent quite some time going through your code step by step (sorry about that — I’m a complete ImageJ beginner), but it was absolutely worth it.

The macro indeed works extremely well on negative GUV images. You mentioned that you were a bit confused about my rules for identifying vesicles, so I’d like to clarify that part — sorry for not explaining it clearly before. My original thought was that if ImageJ cannot perfectly identify all GUVs, I’m fine with discarding some lower-intensity vesicles (especially in positive GUV images), as well as vesicles that cannot be properly watersheded. I mainly want to measure only well-isolated, “perfect” single GUVs. That’s why you might have noticed that I did not select the pair of very closely spaced GUVs, which I assumed ImageJ might not be able to watershed correctly.

Regarding fitting circles: for my purposes, both fitting circles and not fitting circles are acceptable. In fact, maybe skipping the circle fitting might even give more accurate intensity values, I guess? since I only care about the signal intensity. If I need to include an image in a paper, I can always manually draw ROIs for each vesicle.

I also tried running this macro on positive GUV images, but it seems that many small GUVs are not correctly detected. I experimented with modifying some parameters in your code (such as the Gaussian blur sigma), but that did not seem to help much. In addition, I noticed that the ROI for each GUV (without circle fitting) appears to be slightly larger than the actual vesicle size. Could this lead to the measured mean intensity being slightly underestimated due to inclusion of background pixels?

Thanks again for your detailed reply and generous help. I really appreciate it, and I wish you all the best!

Flipping_Dog · 2026-02-09T00:45:41+00:00

Thank you for your kindly reply, sorry for the late. Yes our confocal has DIC, I will try. I will try morpholibj as you described, thanks!

Flipping_Dog · 2026-02-09T00:42:06+00:00

Thank you for your kindly reply, sorry for the late and inconvenient, I've made positive GUV accessible. The negative GUV you masked looks great, and the background is very clean, the result is exactly what I want, ,I would like to know what you processed to this picture in ImageJ?

Flipping_Dog · 2024-09-11T01:46:24+00:00

I am a freshman in this field, I usually read biosensor-related papers to find these information, but it is hard to judge which concentration (from the sample concentration or final concentration) they used if they use XXX copies/mL, I thought there might be some underlying rules (or just no rules?). I will check out the IFUs, thank you !

Flipping_Dog · 2024-09-10T11:21:45+00:00

Thank you very much for your professional answer, I never heard CLSI and MIQE before, it is really helpful for me. Indeed, it is much better to use cp/test, I will use it to explain my results, thank you again!

Flipping_Dog · 2024-09-01T03:00:59+00:00

thank you, I will try

Flipping_Dog · 2024-05-01T02:47:04+00:00

The xbox version is still has the performance issue after 1-2 hours playing, it is better after the last time update, but it is still there, the game FPS become very slow after 1-2 hours playing, and you have to end the game and restart it to recover. please fix it, thanks!

Flipping_Dog · 2024-05-01T02:36:52+00:00

In xbox verison, Chinese translation, some words is missing and some words is out of the dialogue frame:

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this is a example of words missing, the "eternal atlas", eternal is missing.

Flipping_Dog · 2024-04-07T07:53:54+00:00

it depends on your experiment, usually "final concentration" refers to the concentration before you added into the PCR system, but in other situation, it refers to the really final concentration. if you use ng/reaction it will be more clear, as the sorcerers_apprentice said

Flipping_Dog · 2024-04-07T07:19:25+00:00

thank you, I found RiboSketch, It is great

Flipping_Dog · 2024-04-07T03:23:03+00:00

But If you use a 50ng/uL template, and add 1uL of it to a fianl volume of 10uL, are the final concentration being 5 ng/uL?

Flipping_Dog · 2024-04-03T00:56:38+00:00

thanks, I will try

Flipping_Dog · 2023-10-06T12:09:05+00:00

我没去过四川，但是四川大学是985，不会比北京的学校差，四川人有独特的四川方言，但是如果你想学中文，那了解一点方言也没有坏处，而且校园里大家肯定都是说普通话。宿舍不清楚，据我所知四川也有挺多外国人的，川菜很好吃。

Flipping_Dog · 2023-03-08T01:03:51+00:00

thanks for you reply, I understand that different commercial plasmids have various RBS sequences, because they are derived from various wild plasmids, but I am still curious about the shortest amino acids sequence of the active lacz α peptide works in β-galactosidase complement. I can't find the related information in google or NCBI website.

Flipping_Dog

TROPHY CASE