Lecture about Bio-Image Analysis

Dear friends of Bio-Image Analysis,

as a consequence of the COVID-19 situation, I’m recording my lecture about Bio-Image Analysis at the Biotechnology Center of the TU Dresden. Thus, you all can have a look!

The first lession on youtube is about basics and gives an introduction to Fiji.

Stay tuned, I’ll add more lectures weekly until we are allowed to return to the lecture hall. And as always: Feedback is very welcome :slight_smile:

Enjoy!

Cheers,
Robert

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And the coolest thing of all: you yourself are inside a Fiji window! Bravo!

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Finally! :wink:

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@haesleinhuepf
Hi
Thank you for sharing your conference. I look forward to the next ones.

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Thanks a lot for this. After seeing this, I am actually thinking about applying to TU Dresden for MSc in Computational modelling and simulation on the Visual computing track. Would you be kind enough to tell me more about the computer vision opportunities at TU Dresden? I wasn’t able to find a list of modules.

Regards,

Zaigham

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Hey @Zaigham_Randhawa,

the master program you mention has a website:

And there are the list of modules:

The Visual Computing track is organised by Prof. Dachselt:
https://mt.inf.tu-dresden.de/our-group/team/raimund-dachselt/

The Computer Vision activities at TU Dresden are organised by Prof. Bjoern Andres, who just started recently:
https://mlcv.inf.tu-dresden.de/

The lecture I do is part of the Molecular Bioengineering master program at the Biotechnology center headed by Prof. Schroeder. It does not have so much to do with Computer Vision :wink:
http://www.biotec.tu-dresden.de/teaching/masters-courses/molecular-bioengineering/

Let me know if you need more links :wink:

Cheers,
Robert

Oh okay, thanks a lot Prof. Hasse. I really appreciate your help and thanks a lot for putting me in contact with the right people.

Prof. Raimund, I hope you are doing well. I am interested in applying for the MSc CMS program and want to get experience with bio-medical computing (e.g. finding tumors with deep learning) and 3D computer vision for robot-assisted surgery. My life dream is to use motion-capture, 3D-pose-estimation, and hand-gesture-recognition to help automate surgeries. Based on this, I have a couple of questions:

  1. After looking at the details of the curriculum, I am interested in both the visual computing and computational life sciences tracks for MSc comp. modeling, and simulation course. Which one would you recommend? My main interests are in CV/DL, but I need some exposure to the computational life sciences program as well. Is the program flexible enough to allow me to a couple of classes from other tracks as well?

  2. How does TU Dresden cooperate with NCT-Dresden? I saw that there were some masters thesis projects on surgical robotics being offered jointly by both TU-Dresdon and NCT-Dresden.

  3. Does it help if I apply well before the deadline? Some colleges have a rolling admissions policy, while others wait until after the deadline to begin reviewing the application. This is the last month of my final semester and everything is in full swing. I could manage out some time to complete the application by mid-April, but applying after my semester ends (May 7) sounds like a far easier option.

Sorry for so many questions.

Regards,

Zaigham

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@haesleinhuepf
Thank you, for your second series of lessons. It’s really good. I recommend it to those who want an introduction to ImageJ. Hoping to see other series.

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Hi @haesleinhuepf,

Thank you so much for putting your lectures online !

image
Another way of cleaning the ROI manager before or during a macro is to run roiManager("reset"); It has the advantage of resetting it regardless of whether there is a ROI in there or not.

I look forward to the next lectures :slight_smile:

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Awesome, thanks for the hint! I didn’t know about this one. I was always stuggling with the “Delete” command on an empty ROI Manager throwing an error. Now I know how to deal with it easier. Life-long learning! :slight_smile:

Thanks for the feedback, this allows me to improve the lecture!

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Hi @haesleinhuepf,

The link for the code in https://twitter.com/haesleinhuepf/status/1242000971544301568 is broken

Is the script still online ?

I think that in one of your lectures you mention the code, but I couldn’t find in which video it is mentioned…

Thanks

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Hey @LPUoO,

apologies for the inconvenience. Here you go:
https://github.com/clij/clijx/blob/e11fa7bcb199c4f885f5f7342ce4466a25ace960/src/main/macro/interactive_webcam_acquisition_move_rect.ijm

Thanks for testing clij! :slightly_smiling_face:

Cheers,
Robert

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Hi @haesleinhuepf,

This webcam macro is really cool. Next step is facial recognition. :grinning:

Anyway, small comment:
run("CLIJ Macro Extensions", "cl_device=");
needs to be changed to
run("CLIJ2 Macro Extensions", "cl_device=");
Otherwise the macro crashes.

Additionally, on my computer the last choice in the webcam list is actually not a webcam (but a ‘screen recording device’). It results in an immediate complete shutdown of Fiji. How about a dialog to choose the right device?

Bram

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Hey @bramvdbroek,

glad to hear that you like it!

Thanks for the bug report. I just fixed this one!

You know, stuff in CLIJx is known to be a bit buggy. That’s why the “x” stands for experimental there :wink: If you find the time to build such a dialog, I’d be happy to build it in. Or feel free to send a pull-request.

Alternatively, you can also use the webcam-acquisition plugin, which comes with a dialog:

image

Thanks again for your support and feedback!

Have a nice weekend :slight_smile:

Cheers,
Robert

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Hi @haesleinhuepf,

Sorry, I didn’t mean to load you with more work. :slight_smile:
I came to the idea of a dialog because you have it in the plugin. But that’s in JAVA of course…

But I feel some peer pressure now.
Does this code work? (I put away my webcam on my current computer, so can’t test it right now. I’ll send the pull request soon.)
interactive_webcam_acquisition_move_rect_EDIT.ijm (3.4 KB)

Have a nice weekend too!
Bram

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Hi again @haesleinhuepf,

I found some time and updated the script. There is now a proper dialog, including the camera resolution. The code is also a bit optimized here and there, and it works for any ROI shape.
See interactive_webcam_acquisition_move_rect_EDIT2.ijm (4.1 KB).

Do you want me to submit a pull request? (I need to first clone or fork the repository for that, right?)
Otherwise please just check out what you think is useful.

I tried to include a choice of GPU in the same dialog, but that’s not possible because the webcams have to be listed first, using the default GPU. After that re-initializing a GPU results in a JAVA error.
It could be fixed with two dialogs in a row, but that would be a bit overkill for this macro.

Thanks. It was a nice exercise. :grinning:
Bram

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Hey @bramvdbroek,

awesome, thanks for implementing this!

Yes and yes. Maybe this tutorial is helpful.

It would be nice if we could fix this bug together. For a proper bug report, please post a minimal code example which allows me to reproduce the bug. Furthermore, please post the error message. I would also suggest to create a new topic where we can discuss this particular issue.

Thanks again for your support!

Cheers,
Robert

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Hii,
I am a CMS-VC student and an year ago I had the same doubt as yours. I would suggest you to go for VC track as the subjects are not compulsory and you can handpick your courses as per your preference.
Also, in CLS track there are some subjects which are compulsory and pretty dull, like Biochemistry which you have to pass inorder to clear certain modules,

If you need more information email Prof Gumhold. He is head of computer graphics chair at TU Dresden. All the best

Hey Faraz,
Thanks a lot for your reply, appreciate it. Fortunately, I was offered, and have accepted, a position as a Ph.D. candidate at West Virginia Uni in biomedical applications of CV. Even though I would have loved to come to TU Dresden, as a Pakistani who had just completed his bachelor’s in the US, traveling back to Pakistan and getting the german visa wasn’t the safest of the options because of the pandemic. Hopefully, I would apply for summer-internships/Post-Doc positions later on at your place and be able to visit and work at TU Dresden. If you wanna, please do add me on LinkedIn.
Regards,
Zaigham