Great video. I am trying to overlap two spatial transcriptomics plots scatter plots, but I am unable to change the LUT to gray, since they are RBG images. Thus, I cannot threshold. What would you suggest in these cases?
Hello. If you split the RGB image into channels, the resulting images will be 8-bit. You can then change the LUT of the channels you are interested in.
Hi @dr.sandeshkamdi4601. Yes, % overlap can be computed from the overlap area normalized to the area of either one of your objects (GAD or cFOS). Note, however, that the %overlap is an overall value. If you want to get individual overlap percentages, you can try DiAna (th-cam.com/video/CBwWk7wP2kQ/w-d-xo.htmlsi=BOS8bozq90Gl4xAo).
Hi Johanna, thank you for your tutorials; they're very helpful. I was wondering if there's a way to know how many overlaps I have per image and the area of each overlap.
Hi there! Have you checked out colocalization with JACoP? Or DiAna? FIJI (ImageJ): Measuring Colocalization [JACoP BIOP Version] th-cam.com/video/dk3ETh8oSX0/w-d-xo.html FIJI (ImageJ): Colocalization & Distance Analysis with DiAna [I. 2D Multi-Channel Images] th-cam.com/video/CBwWk7wP2kQ/w-d-xo.html
Thank you, Johanna!!!! Your video is perfect for me! I have one question how to calculate the % overlap. I got results (Area, IntDen, %Area, and RawIntDen value) following this video, but i don't know how to get the final overlap value. Could you help me?
Hi jjem Soh@thwoals456. If you export your results to excel, the % overlap can be calculated by dividing the overlap area by the area covered by the objects in a particular channel.
Hi Joy. The ROI Manager is generally used for 2D images. For z stacks, doing colocalization analysis might be a better option. I’ll try to come up with a tutorial on measuring overlap on z stacks. Thanks for watching.
is it possible to have your mail ID, respected ma'am? i don't know almost anything of ImageJ but all of a sudden i realize that some of these might work for my thesis and hence bothering you.
Hi Johanna. Thank you for posting this tutorial. Your channel is amazing and very helpful for those working in microscopy like me. I want to apply this measurement of overlap using the ROI manager for an experiment in an upcoming publication and I was wondering if you know about studies that have used this analysis to cite them in my paper. Thank you in advance, Rafael.
Hi Johanna. Thanks for the video, really helpful :) By chance, do you have a macro that can run the whole process automatically and that you wouldn´t mind to share?
@carmenm.dominguez3058 Hi Carmen. Thanks for watching. I don't have a macro for this specifically, but you can use the macro recorder to record the steps to go through the whole process. Once you have this, you can apply this to another image.
@AnduneYavetil, thanks for your support. This isn't something new...just wanted to make it easier for ImageJ/Fiji users to check out tools to do image analysis.
![FIJI (ImageJ): Colocalization & Distance Analysis with DiAna [I. 2D Multi-Channel Images]](http://i.ytimg.com/vi/CBwWk7wP2kQ/mqdefault.jpg)
![FIJI (ImageJ): Colocalization & Distance Analysis with DiAna [I. 2D Multi-Channel Images]](/img/tr.png)
Your videos are, bar-none, the most actually helpful instructions in the use of FIJI (ImageJ) are have found. Super thanks!
Thank you @Mo11usq. I really appreciate you taking the time to express that.
Great video. I am trying to overlap two spatial transcriptomics plots scatter plots, but I am unable to change the LUT to gray, since they are RBG images. Thus, I cannot threshold. What would you suggest in these cases?
Hello. If you split the RGB image into channels, the resulting images will be 8-bit. You can then change the LUT of the channels you are interested in.
@@johanna.m.dela-cruz That worked, thank you
I have cFOS and GAD cells to calculate the overlap between them. So % overlap would be
Overlap area/ area of GAD or cFOS? what should be the formula?
Hi @dr.sandeshkamdi4601. Yes, % overlap can be computed from the overlap area normalized to the area of either one of your objects (GAD or cFOS). Note, however, that the %overlap is an overall value. If you want to get individual overlap percentages, you can try DiAna (th-cam.com/video/CBwWk7wP2kQ/w-d-xo.htmlsi=BOS8bozq90Gl4xAo).
Ji Johana, Thanks for the tutorial. The interpretation part is missing to calculate the % overlap. Please add that part.
Please check my reply in your other comment.
Hi Johanna, thank you for your tutorials; they're very helpful. I was wondering if there's a way to know how many overlaps I have per image and the area of each overlap.
Hi there! Have you checked out colocalization with JACoP? Or DiAna?
FIJI (ImageJ): Measuring Colocalization [JACoP BIOP Version]
th-cam.com/video/dk3ETh8oSX0/w-d-xo.html
FIJI (ImageJ): Colocalization & Distance Analysis with DiAna [I. 2D Multi-Channel Images]
th-cam.com/video/CBwWk7wP2kQ/w-d-xo.html
@@johanna.m.dela-cruz Thank you so much, Johanna; you're the best. I'll take a look into those plugins.
Thank you, Johanna!!!! Your video is perfect for me! I have one question how to calculate the % overlap. I got results (Area, IntDen, %Area, and RawIntDen value) following this video, but i don't know how to get the final overlap value. Could you help me?
Hi jjem Soh@thwoals456. If you export your results to excel, the % overlap can be calculated by dividing the overlap area by the area covered by the objects in a particular channel.
@@johanna.m.dela-cruz yeah, but what's the overlap Area?
@@andreadalessandro2548 If you check from 03:32 of the video, this explains how the overlap can be measured from the ROI Manager.
Great efforts 👏🏻👏🏻👏🏻
Thank you @hamza for your kind words.
Does it work for multiple slides at once w/ z stack?
Hi Joy. The ROI Manager is generally used for 2D images. For z stacks, doing colocalization analysis might be a better option. I’ll try to come up with a tutorial on measuring overlap on z stacks. Thanks for watching.
@@johanna.m.dela-cruz gotcha, thanks
is it possible to have your mail ID, respected ma'am? i don't know almost anything of ImageJ but all of a sudden i realize that some of these might work for my thesis and hence bothering you.
Hi there. You can find my email in my channel page (About section).
@@johanna.m.dela-cruz thanks a lot ma'am; just emailed you.
Hi Johanna. Thank you for posting this tutorial. Your channel is amazing and very helpful for those working in microscopy like me. I want to apply this measurement of overlap using the ROI manager for an experiment in an upcoming publication and I was wondering if you know about studies that have used this analysis to cite them in my paper. Thank you in advance, Rafael.
Hi Rafael. Thank you for your inspiring comments.
You can check the link imagej.net/contribute/citing to cite ImageJ or Fiji.
Hi Johanna. Thanks for the video, really helpful :) By chance, do you have a macro that can run the whole process automatically and that you wouldn´t mind to share?
@carmenm.dominguez3058 Hi Carmen. Thanks for watching. I don't have a macro for this specifically, but you can use the macro recorder to record the steps to go through the whole process. Once you have this, you can apply this to another image.
@@johanna.m.dela-cruz that´s a great idea :D i will try that. Thanks a lot of the tip!
You should publish this in Jove so I can cite you!
@AnduneYavetil, thanks for your support. This isn't something new...just wanted to make it easier for ImageJ/Fiji users to check out tools to do image analysis.