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Questions tagged [imagej]

Questions about the popular image analysis platform ImageJ.

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Building a better cell detection interface

First of all, i dont know if the following request is allowed within the guidelines of stackExchange, but i will post it and delete it if deemed necessary. I am a student (computer science) who was ...
one_of_8_billion_people's user avatar
4 votes
2 answers

Suggestion on program/algorithm to segment nuclei

I've got some images such as the one in this post, obtained from the neuroepithelium of a chick embryo in a confocal microscope, where nuclei have been fluorescently labeled. I'd like to be able to ...
Santiago Bosch's user avatar
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Looking for a way to create a video or animated image of a series of segmented lines with cells in ImageJ

I considered asking this on software recs, but felt that the biology community would know better if ImageJ was capable of doing something this way, so I'm asking here. I'm trying to do a project with ...
Andrew's user avatar
  • 71
-1 votes
1 answer

Need help with ImageJ thresholding

I'm trying to measure the colocalization of two proteins in a .tiff image taken with a wide-field fluorescence microscope. In ImageJ I have split the image into the two channels (red and green), and ...
betelgeuse's user avatar
1 vote
3 answers

How to create a 3D density map of a system of varying number of particles?

I have a time-dependent system of varying number of particles (~100k particles). In fact, each particle represents an interaction in a 3D space with a particular strength. Thus, each particle has (X,Y,...
deeep's user avatar
  • 13
2 votes
0 answers

background extraction in microscope analysis

I have taken microscope pictures for proteins in HeLa cells, in order to quantify the intensity (immunofluorescence). The proteins are both at the nuclear envelope, and in order to quantify the ...
Katz's user avatar
  • 1,013
3 votes
2 answers

How to set threshold in ImageJ for quantifying relative fluorescence?

I have taken images from two different samples that have uptaken EdU during DNA synthesis (S-phase). The experiment setup is to find which condition had uptaken more EdU. Therefore I am detecting EdU ...
Parham's user avatar
  • 33
2 votes
1 answer

Can I use grayscale images when working with ImageJ?

I am using ImageJ to analyze Western Blots. I have scanned films in as grayscale images because this is how we did it in my old lab. People in my current lab are not satisfied with that explanation ...
Slavatron's user avatar
  • 1,010
4 votes
1 answer

How to remove bad lanes in ImageJ Westernblot analysis

I use ImageJ to do an analysis of a Westernblot Image. If everything goes as wanted the workflow is fine. But if I do something wrong creating a lane there is no undo for a lane and also no way to ...
Janusz's user avatar
  • 91