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May 11, 2021 07:05 PM | Ruqiang Liang
synapse finding
I am new on Vaa3D. In Imaris we can add point structures to find
all point synapses quite fast. I tried with Vaa3D auto cell
segmentation trying to mimic Imaris but cannot accurately locate
synapses. Are there any plugins I can use to mimic that Imaris
function? Thanks.
Best/ Ruqiang
Best/ Ruqiang
May 12, 2021 01:05 PM | Yimin Wang
RE: synapse finding
Hi Ruqiang,
Thanks for your interest in trying Vaa3D.
However, I have limited experiences in Imaris, thus not quite sure what exact function you are referring to.
Could you give more explanation about what does Imaris do and what is the step by step procedure for that?
Thanks!
Best,
Yimin
Thanks for your interest in trying Vaa3D.
However, I have limited experiences in Imaris, thus not quite sure what exact function you are referring to.
Could you give more explanation about what does Imaris do and what is the step by step procedure for that?
Thanks!
Best,
Yimin
May 14, 2021 04:05 PM | Ruqiang Liang
RE: synapse finding
HI Yimin,
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
May 17, 2021 06:05 AM | Yimin Wang
RE: synapse finding
Hi Ruqiang,
From the snapshot, I assume that the green spots represent synapses and you intend to identify and count hem automatically from a 2D image?
Best,
Yimin
Originally posted by Ruqiang Liang:
From the snapshot, I assume that the green spots represent synapses and you intend to identify and count hem automatically from a 2D image?
Best,
Yimin
Originally posted by Ruqiang Liang:
HI Yimin,
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
May 17, 2021 06:05 PM | Ruqiang Liang
RE: synapse finding
HI Yimin,
No, I want to identify and count them from 3D Zstack. Ideally report X, y, Z, and size. Is this possible? I tried with cell_counting plugin from Vaa3D before. Tt was cell_counting -> quickFind -> Exemplar definition and propagation, but not too much success. I guess it depends on the representative of the examples.
Thanks.
Best/ Ruqiang
Originally posted by Yimin Wang:
No, I want to identify and count them from 3D Zstack. Ideally report X, y, Z, and size. Is this possible? I tried with cell_counting plugin from Vaa3D before. Tt was cell_counting -> quickFind -> Exemplar definition and propagation, but not too much success. I guess it depends on the representative of the examples.
Thanks.
Best/ Ruqiang
Originally posted by Yimin Wang:
Hi Ruqiang,
From the snapshot, I assume that the green spots represent synapses and you intend to identify and count hem automatically from a 2D image?
Best,
Yimin
Originally posted by Ruqiang Liang:
From the snapshot, I assume that the green spots represent synapses and you intend to identify and count hem automatically from a 2D image?
Best,
Yimin
Originally posted by Ruqiang Liang:
HI Yimin,
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
May 18, 2021 05:05 PM | Yimin Wang
RE: synapse finding
Hi Ruqiang,
Unfortunately, this plugin probably lost maintenance over time.
Maybe you or someone else in the community could help to improve the code.
Best,
Yimin
Originally posted by Ruqiang Liang:
Unfortunately, this plugin probably lost maintenance over time.
Maybe you or someone else in the community could help to improve the code.
Best,
Yimin
Originally posted by Ruqiang Liang:
HI
Yimin,
No, I want to identify and count them from 3D Zstack. Ideally report X, y, Z, and size. Is this possible? I tried with cell_counting plugin from Vaa3D before. Tt was cell_counting -> quickFind -> Exemplar definition and propagation, but not too much success. I guess it depends on the representative of the examples.
Thanks.
Best/ Ruqiang
Originally posted by Yimin Wang:
No, I want to identify and count them from 3D Zstack. Ideally report X, y, Z, and size. Is this possible? I tried with cell_counting plugin from Vaa3D before. Tt was cell_counting -> quickFind -> Exemplar definition and propagation, but not too much success. I guess it depends on the representative of the examples.
Thanks.
Best/ Ruqiang
Originally posted by Yimin Wang:
Hi Ruqiang,
From the snapshot, I assume that the green spots represent synapses and you intend to identify and count hem automatically from a 2D image?
Best,
Yimin
Originally posted by Ruqiang Liang:
From the snapshot, I assume that the green spots represent synapses and you intend to identify and count hem automatically from a 2D image?
Best,
Yimin
Originally posted by Ruqiang Liang:
HI Yimin,
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang
Thank you so much for the swift reply. Here is a snapshot of the result showing in Imaris Viewer. My assistant did this analysis and I just found that it isn't quite accurate. I just want to get the center of each spot labeled by green fluorescence. Any suggestions? Thanks.
Best/ Ruqiang