Thank you so much!! Your video made it easier for me as someone new to imageJ. I followed through the steps and have 5 channels, after segmenting the cells, I want to find out if the cells our positive for other marker. Is that possible?
Hi Misha (@meesha5883). Thanks for your continued support. If you have your segmented cells added into the 3D ROI Manager, you can select these ROIs and apply them to your other channel, then do your measurements (just like you would on the original channel where the cells were segmented).
@@johanna.m.dela-cruz thank you for responding, I managed to apply the segmentation to another channel but how do I do thresholding for that channel (and add positive label for that marker to positive cells). Another problem is that the segmentation used nuclear stain and I want to dilate the ring of segment ring for each cell so that I can measure the marker that are expressed in the local cell area not just nucleus. I want to output a csv file with cells coordinates and info if they are positive for any of the markers.
@meesha5883 I believe you posted this question in the image.sc forum. For a label image stack, you can use MorphoLibJ. Go to Label > Label Edition. Dilate the objects (as many times as you like), then press done. You can then add the new label stack to the 3D Manager.
Wow thanks you so much !! you saved me for my internship ! Do you know if there is a way to automatize all these (with a python script, for example) so we can do it with several images ?
I also have a problem when i try to segment nuclei. if the are close in the stack (like one under another) , they are considered as 1 nuclei, do you know how can i solve this ?
@Melissa-ts9mx Does thresholding work on your images? Check out my latest tutorial on applying a watershed to split connected objects. StarDist works well for 2D images since you can adjust parameters. Unfortunately, Stardist-Trackmate uses specific parameters that can't be modified in TrackMate.
@@johanna.m.dela-cruz I just tried the tutorial, it work better ! Indeed, i have a problem; some nuclei are splitted so i have much more nuclei that i am supposed to have. Do you know how can I improve the segmentation with your latest video ? How could i choose a diameter or something like that ?
hi..Thank you for the video. I was wondering if its possible to get only the 3D mask from these z stack. Like I just want the 3D mask from my 3D stack of images. Thank you
I'm playing a bit with this approach for segmenting a z-stack of neurons in fluorescence microscopy from a brain slice. I noticed a problem that I don't know how to solve. Maybe you could give me a hint. In my images, it often happens that neurons disappear at a certain z plane and a new neuron appears underneath. The tracker however considers these situations as one single neuron (I get one single continuous track) so in the end the number of cells that I get is lower compared to the number of neurons that are really there. I've tried several trackers and several parameters but the result is always the same. Any idea how I could solve this?
![FIJI (ImageJ): Trainable Weka Segmentation 3D [Working with Image Stacks or Sequences]](http://i.ytimg.com/vi/pfKujV_pOww/mqdefault.jpg)
Thank you so much!! Your video made it easier for me as someone new to imageJ. I followed through the steps and have 5 channels, after segmenting the cells, I want to find out if the cells our positive for other marker. Is that possible?
Hi Misha (@meesha5883). Thanks for your continued support. If you have your segmented cells added into the 3D ROI Manager, you can select these ROIs and apply them to your other channel, then do your measurements (just like you would on the original channel where the cells were segmented).
@@johanna.m.dela-cruz thank you for responding, I managed to apply the segmentation to another channel but how do I do thresholding for that channel (and add positive label for that marker to positive cells). Another problem is that the segmentation used nuclear stain and I want to dilate the ring of segment ring for each cell so that I can measure the marker that are expressed in the local cell area not just nucleus. I want to output a csv file with cells coordinates and info if they are positive for any of the markers.
@meesha5883 I believe you posted this question in the image.sc forum. For a label image stack, you can use MorphoLibJ. Go to Label > Label Edition. Dilate the objects (as many times as you like), then press done. You can then add the new label stack to the 3D Manager.
Wow thanks you so much !! you saved me for my internship ! Do you know if there is a way to automatize all these (with a python script, for example) so we can do it with several images ?
I also have a problem when i try to segment nuclei. if the are close in the stack (like one under another) , they are considered as 1 nuclei, do you know how can i solve this ?
@Melissa-ts9mx Does thresholding work on your images? Check out my latest tutorial on applying a watershed to split connected objects. StarDist works well for 2D images since you can adjust parameters. Unfortunately, Stardist-Trackmate uses specific parameters that can't be modified in TrackMate.
For scripting, you might want to check this out: imagej.net/plugins/trackmate/scripting/scripting.
@@johanna.m.dela-cruz I just tried the tutorial, it work better ! Indeed, i have a problem; some nuclei are splitted so i have much more nuclei that i am supposed to have. Do you know how can I improve the segmentation with your latest video ? How could i choose a diameter or something like that ?
@@Melissa-ts9mx Perhaps it might be better if you send me an email with a copy of your image?
hi..Thank you for the video. I was wondering if its possible to get only the 3D mask from these z stack. Like I just want the 3D mask from my 3D stack of images. Thank you
@@MDIqbalHossain-d8v hi! You can convert the label image stack into a binary stack by thresholding. Use a minimum threshold of 1.
Oh my God! Thank you! Thank you! Thank you!!! I was about to give up but you just saved me! :'D
Happy to help. 😊
I'm playing a bit with this approach for segmenting a z-stack of neurons in fluorescence microscopy from a brain slice. I noticed a problem that I don't know how to solve. Maybe you could give me a hint. In my images, it often happens that neurons disappear at a certain z plane and a new neuron appears underneath. The tracker however considers these situations as one single neuron (I get one single continuous track) so in the end the number of cells that I get is lower compared to the number of neurons that are really there. I've tried several trackers and several parameters but the result is always the same. Any idea how I could solve this?
@@franc_giann the neurons are probably still connected in 3d. Try getting a z projection of your stack…do the neurons seem like they’re connected?