Thank you for this tutorial, is exactly what I needed. Also, I followed the link to the 3D model that you linked in a comment and it has the reference to the paper. I would suggest that you include that kind of link in the information box, it makes really easy to cite your work when we use your methods.
Hi, thanks. It’s very much dependent on the data. I have some data for which the Standard Deviation works really well. Max Intensity works well if you are interested in the brightest structures. Just depends really.
Hi, yes you need to combine single images into a stack (‘images to stack’ menu option) before you can perform a z-projection. This should work with any valid file type.
Thank u for the video. I have several paste with images to do z project...can you program the image j to do Al the carpets instead of selecting one at each time
Yes, it was. The trichomes were embedded in amber (20 million years old?) and were scanned using confocal laser scanning microscopy. From memory, I think it was a x4 objective. Totally amazed it actually worked. Further details and 3D model can be found here; sketchfab.com/3d-models/plant-trichomes-embedded-in-amber-cc9423669b4244839e0b3e8f4e24caa1
Thank you for this tutorial, is exactly what I needed. Also, I followed the link to the 3D model that you linked in a comment and it has the reference to the paper. I would suggest that you include that kind of link in the information box, it makes really easy to cite your work when we use your methods.
Hi, thanks. I have added the link. Thanks for the suggestion and for watching. C.
Thank you so much! Very informative!
Thank you very much for this.
Very nice explanation, thank you very much. I just wonder why it is preferable using maximum intensity over average intensity
Hi, thanks. It’s very much dependent on the data. I have some data for which the Standard Deviation works really well. Max Intensity works well if you are interested in the brightest structures. Just depends really.
you used a pic file. does it work for JPEG or TIFF files also. if yes, what we need to do before going to Z projection, As it says "Needs Stacking"
Hi, yes you need to combine single images into a stack (‘images to stack’ menu option) before you can perform a z-projection. This should work with any valid file type.
Thank u for the video.
I have several paste with images to do z project...can you program the image j to do Al the carpets instead of selecting one at each time
Hi, Sorry, I dont quite follow the question. Can you elaborate a little more? Thanks.
thank you for your explanation. It was very informative, although the first three minutes could be condensed.
Thanks Alex, I’m always thankful for constructive feedback. Still on the learning curve with these.
Would you explain how the plant image was actually made? Was it a stacked image set?
Yes, it was. The trichomes were embedded in amber (20 million years old?) and were scanned using confocal laser scanning microscopy. From memory, I think it was a x4 objective. Totally amazed it actually worked. Further details and 3D model can be found here; sketchfab.com/3d-models/plant-trichomes-embedded-in-amber-cc9423669b4244839e0b3e8f4e24caa1