Asking help on Tango from a bioinformation newbie

tango
Tags: #<Tag:0x00007fd53fde9a60>

#1

Dear Sir @ThomasBoudier

I am a bioinformation newbie. I tried to mail you to thomas.boudier@snv.jussieu.fr, but the mail was returned. So I post my question here and wish to get your help. I think Tango is a very good tool for our researcher in Bio field. It is so great that you published it early in 2014.

I am trying to use Tango for measuring cell’s diameter for my research. But I encountered some problem when I was learning using Tango. When I ran the processing in “Field” stage, there is always some java enviroment error like missing imageware class (i guess) (Fig 1 attached). And nucleus doesn’t show correctly and centromeres doesn’t show up in the 3D viewer for the sample image (Fig 2 attached). So I searched the internet and found an announcement titled with “EPFL BIG plugins moved to their own update site” in the ImageJ forum (EPFL BIG plugins moved to their own update site). The announcement mentioned that imageware was isolated because of the license problem.

My question is
1 Is Tango still working?
2 If Tango is still working, do you think the problem I encountered is because of the license problem of imageware?
3 If yes, how can I make Tango work.

You are appriciated if you can help me figure out this problem, since it is very important for my research. I am waiting for your reply.

Thank you and wish your the best

Mable


#2


@ThomasBoudier
I forgot to attache the figures.


#3


@ThomasBoudier
I forgot to attache the figures.


#4

Dear @mable,

TANGO is still working, tough is not so active as it used to be, it is still slowly developed. Thanks for your message I was not aware of the change for ImageWare, note that TANGO uses ImageWare only for LOG filtering, I may suggest alternatives to this filter such as 3D Gaussian or 3D Median.
If you have more questions related to TANGO please contact me directly with the email shown on my plugins webpage 3D ImageJ Suite

Best,

Thomas.


#5

Hi @mable and welcome to the forum!

Glad that you found this announcement. Did you actually try if TANGO works fine after enabling the BIG-EPFL update site as mentioned in that discussion?
As the plugins really only moved from the Fiji update site to the EPFL one, everything should work as expected with the BIG-EPFL update site enabled.

Did you know that on Windows, you can copy a single-window screenshot to the clipboard by pressing AltPrint Screen? You can just paste this into the forum here, no need to go via mobile phone cam :wink:

Also, for looking at your exception, it is much more helpful if you simply copy and paste the text from the console window, instead of pasting a screenshot.


@ThomasBoudier @mable please keep the discussion open, your solutions can be helpful for others having the same issue in the future. That’s why we have this forum!


#6

Dear @ThomasBoudier @imagejan

I am so excited and glad that I got reply from both of you. Thank you for your time on replying me.:grinning:
I have tried both to use 3D Gaussian or 3D Median filter instead of LOG filtering and to enable the BIG-EPFL update site, there isn’t error about imageware any more. But it seems structure processing still doesn’t work. The processing is stuck on the first cell for almost hours . (as figure 3 shows which is a screen shot:stuck_out_tongue:).

I hope I can still have your reply.
Thank you and wish you the best.
Mable


#7

Dear @ThomasBoudier
I forgot to ask the question directly. Do you have any idea about the reason why the processing is stuck for almost a whole night. (By the way the memory of my computer support 4 threads.) Is it normal?
Looking forward to your reply.
Thank you and wish you the best.
Mable


#8

Dear @mable,

Glad to see the pb with imageware is solved. For TANGO I would recommend to first extract the cells (or nuclei) from the field image with process nuclei and crop cells, and then test the procedure to extract the structures that are within nuclei on one nucleus first.
What is your procedure ?

Best,

Thomas


#9

Dear @ThomasBoudier,
Thank you for your reply. I can process the structure , such as chromosome now. The processing can smoothly move on, and the structure can be shown up. But there is still a problem that the edge of the nucleus is of square shape, even I use the sample image and the corresponding process chain provided by Tango website. I have no idea how to deal with this problem. You are appreciated if you can help on it. Looking forward your reply.
Best,
Mable
nucleus


#10

Dear @ThomasBoudier,
Just found your update of change log. The 3D image of sample nucleus is so beautiful. The update is very helpful and timely. Thank you so much.:grinning::+1::+1:
best,
Mable