Hi, I am not able to get the Cell Filter preview, ie. the yellow outline as I was trying out the plugin with the test images. Any idea what could be going wrong?
Very nice tutorial and plug in. I tried with the test images option, but when I am going to look at the Preview in "cell filters" step (I followed the same as in the video), I get a message Log: ParticleAnalyzer: threshold not set; assumed to be 255-255. Any idea why and how to solve it?
Nice plugin and very clearly explained in the video. I am trying to figure out how to use this plugin in order to to count the number of cells that co-express two reporters (mCherry and GFP). Any ideas on this?
Hi. Thanks for this plugin, it's very powerful and easy to use. I'm trying to run this inside a macro (so it analyses each pair of images in a folder) but each time Analyze is selected it opens a new results table, meaning that I get a new results table for each image pair. Is there a way to make results from each Analyze step appear in the same results table?
Really nice plugin. Dumb question but I'm installing the .jar into the plugins folder and restarting FIJI but not getting the plugin? Installed other plugins this way fine earlier.
Not a dumb question at all! Make sure you have deleted the numbers and hyphen after the .jar file. For example, rename EzColocalization_.jar- 2018031210358 to just "EzColocalization_.jar".
We don't provide counting measurements of colocalized puncta because one key point of the metric we use is to take into account the probability of observing overlaps by chance. Simply counting the number of overlaps doesn't consider the probability of observing overlaps by chance. It's not difficult to use provided ImageJ functions to count the number of overlapped particles between 3 channels. You can 1. Threshold your images in Image -> Adjust -> Threshold. 2. create a composite RGB color image with 3 thresholded binary images in Image -> Color -> Merge Channels... Red, Blue, Green 3. Threshold your color images with the color threshold that all 3 colors all exist. in Image -> Adjust -> Color Threshold. 4. Convert the thresholded RGB to binary in Image -> Type -> 8 bit. 5. Count the number of overlapping regions by analyzing particles in Analyze -> Analyze Particle.
Yes. You can try ImageJ Macro following the instruction from here by recording your actions and editing it. imagej.nih.gov/ij/developer/macro/macros.html#recorder
Hi, I am not able to get the Cell Filter preview, ie. the yellow outline as I was trying out the plugin with the test images. Any idea what could be going wrong?
I'm having the same issue now. Is there any solutions for that?
Settings -> Parameters -> Check " Use Manual background settings below" and only this one. It worked for me at least.
Hey, I am loving this tool. I was wandering if there is a way to change the colors and the style of the scatterplot directly from the plugin.
Very nice tutorial and plug in. I tried with the test images option, but when I am going to look at the Preview in "cell filters" step (I followed the same as in the video), I get a message Log: ParticleAnalyzer: threshold not set; assumed to be 255-255. Any idea why and how to solve it?
Nice plugin and very clearly explained in the video. I am trying to figure out how to use this plugin in order to to count the number of cells that co-express two reporters (mCherry and GFP). Any ideas on this?
Hi. Thanks for this plugin, it's very powerful and easy to use. I'm trying to run this inside a macro (so it analyses each pair of images in a folder) but each time Analyze is selected it opens a new results table, meaning that I get a new results table for each image pair. Is there a way to make results from each Analyze step appear in the same results table?
You can rescale the image in Image->Scale... Choose a number greater than one.
Really nice plugin. Dumb question but I'm installing the .jar into the plugins folder and restarting FIJI but not getting the plugin? Installed other plugins this way fine earlier.
Not a dumb question at all! Make sure you have deleted the numbers and hyphen after the .jar file. For example, rename EzColocalization_.jar- 2018031210358 to just "EzColocalization_.jar".
Could you use this tool to quantify the number of colocalized puncta between 3 channels?
We don't provide counting measurements of colocalized puncta because one key point of the metric we use is to take into account the probability of observing overlaps by chance.
Simply counting the number of overlaps doesn't consider the probability of observing overlaps by chance.
It's not difficult to use provided ImageJ functions to count the number of overlapped particles between 3 channels.
You can
1. Threshold your images in Image -> Adjust -> Threshold.
2. create a composite RGB color image with 3 thresholded binary images in Image -> Color -> Merge Channels... Red, Blue, Green
3. Threshold your color images with the color threshold that all 3 colors all exist. in Image -> Adjust -> Color Threshold.
4. Convert the thresholded RGB to binary in Image -> Type -> 8 bit.
5. Count the number of overlapping regions by analyzing particles in Analyze -> Analyze Particle.
very nice plugin. Easy to work with. Just a question, do it have a batch processor to analyze several images semi-automatically?
Yes. You can try ImageJ Macro following the instruction from here by recording your actions and editing it. imagej.nih.gov/ij/developer/macro/macros.html#recorder