Hi , thank you very much for this video, i was wondering if i can use this method to measure area fraction of a signal after thresholding on a Z stack ? Thanks
Hi @Myriem OTMANI IDRISSI. Thanks for watching. For z stacks, instead of area, the volume is measured from both the 3D Objects Counter and 3D Manager. I don't think there is a direct way to measure the volume fraction. You might have to use the 3D Manager - under 3D Segmentation you will need to threshold the whole image stack (using 0 as low threshold and 255 as high threshold, if you have an 8-bit stack). After adding the segmented stack into the Manager, The Measure 3D button gives the volume of the whole stack (background and objects included). You can then calculate the volume percent by dividing the total volume of your objects by the total volume of the stack. Hope this helps.
@@sriti_hikari Since each image in a z-stack is an optical section of your sample, fiber orientation shows the angle per slice. If you do a maximum projection of your z stack and then run the plugin, the orientation is based on the xy plane.
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I must say, I use Fiji quite often, and still learn new stuff on your channel. Keep up with the good work!
Thanks, @MOLECULARBILL.
This was REALLY helpful! Thank you for making this video and I love the happy music lol
My pleasure. Thanks for listening, watching and learning. 😊
Thanks very much for the excellent FIJI instruction. ^_^
Thanks for watching, @Qingbo Wang. Comments like yours inspire me to continue with my series.
Thanks, It's really help for me.
Glad to help. Thanks for watching.
with 3d object counter, can we obtain the position (x,y,z) in the result sheet?
Hi @nalar150. If you add Centroid (or center of mass) in the 3D OC Options, you can get coordinates of the centers of each object detected.
Hi , thank you very much for this video, i was wondering if i can use this method to measure area fraction of a signal after thresholding on a Z stack ? Thanks
Hi @Myriem OTMANI IDRISSI. Thanks for watching. For z stacks, instead of area, the volume is measured from both the 3D Objects Counter and 3D Manager. I don't think there is a direct way to measure the volume fraction. You might have to use the 3D Manager - under 3D Segmentation you will need to threshold the whole image stack (using 0 as low threshold and 255 as high threshold, if you have an 8-bit stack). After adding the segmented stack into the Manager, The Measure 3D button gives the volume of the whole stack (background and objects included). You can then calculate the volume percent by dividing the total volume of your objects by the total volume of the stack.
Hope this helps.
@@johanna.m.dela-cruz Thank you very much, i will be trying this
Is there any way I can contact you about resolving my issues? I'm stuck at "Step 2/3 Connecting Structures" and I haven't found a solution in days.
@sikEyy. Go to my channel. In the 'About' page, you can find my email.
@@johanna.m.dela-cruz Thank you! Sent the email
Thanks, how can i determine the x y z coordinate pf these particles or cells in 3D
Hi @waelhamda. You will need to set your measurements so that they would include either the centroid or center of mass of the objects.
Amazingggg🌸🌸
Hi do you have any idea on how to measure the fiber orientation on a 3d-z-Stack?
@@sriti_hikari You can try Directionality or OrientationJ. My tutorial is here: ruclips.net/video/tN0bEVsumJc/видео.htmlsi=vxeAMMU906Wsts0z
@@johanna.m.dela-cruz Hi thank you for your help- this will only give the orientation in the x-y-plane right? so the direction in z is not considered?
@@sriti_hikari Since each image in a z-stack is an optical section of your sample, fiber orientation shows the angle per slice. If you do a maximum projection of your z stack and then run the plugin, the orientation is based on the xy plane.
Can you create a mask out of that segmentation?
Hi Octavia (@octaviasantisl). A labeled image/stack can be converted into a binary mask by using a low threshold of 1.