Re: [DIYbio] Camera for fluorescence detection system

" Is the light from one particle varying a lot if it is against the far wall of the tube or near wall?"

Unfortunately, I don't know, whether the light is varying or not depending on the position of the particle. I am developing the system from the scratch and there is almost no experience with fluorescence at my institute. 

"Will there be a low low chance of two touching or close to each other?"

I think, the chance will be quite high...
These particles have the same emission spectrum. But my filter set is interchangeable, so separate measurements with particles with different emission spectra can be conducted.

"Are you wanting to do any hardware or code development, or just "full manual" proof of concept?"

Some code will also be part of my setup. I want to display the sensor data. My initial thought was getting the intensities of my cameras pixels, calculating the average value, normalizing it to some kind of maximum and then plotting it.

Charles

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Re: [DIYbio] Camera for fluorescence detection system

almost sounds like capillary electrophoresis - ...

On Tue, Nov 24, 2020 at 11:01 AM John Griessen <john@industromatic.com> wrote:
On 11/23/20 4:23 PM, 'Charles Maldonado' via DIYbio wrote:
> The moving particles are in a tube with fixed wall thickness. These particles are only moving in one direction and have a constant
> speed. So it's fine that I only measure the fluorescence directly in front of my sensor. I have to detect their presence/absence.
> I am triggering the fluorescence by illuminating the particles with light from a LED. I want to place my sensor perpendicular to
> the light source.

Since you say you don't need to know how strongly they glow, or if there are two of them clumped together, you could get away
without image processing.

" I only have to detect one fluorophore. "

Will there be a low low chance of two touching or close to each other?

If so, the sensor route is good.  You might even be able to detect when two are in the field of view by relative intensities.  Is
the light from one particle varying a lot if it is against the far wall of the tube or near wall?  Are you wanting to do any
hardware or code development, or just "full manual" proof of concept?

John

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Re: [DIYbio] Camera for fluorescence detection system

On 11/23/20 4:23 PM, 'Charles Maldonado' via DIYbio wrote:
> The moving particles are in a tube with fixed wall thickness. These particles are only moving in one direction and have a constant
> speed. So it's fine that I only measure the fluorescence directly in front of my sensor. I have to detect their presence/absence.
> I am triggering the fluorescence by illuminating the particles with light from a LED. I want to place my sensor perpendicular to
> the light source.

Since you say you don't need to know how strongly they glow, or if there are two of them clumped together, you could get away
without image processing.

" I only have to detect one fluorophore. "

Will there be a low low chance of two touching or close to each other?

If so, the sensor route is good. You might even be able to detect when two are in the field of view by relative intensities. Is
the light from one particle varying a lot if it is against the far wall of the tube or near wall? Are you wanting to do any
hardware or code development, or just "full manual" proof of concept?

John

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Re: [DIYbio] Camera for fluorescence detection system


Thanks a lot for all of your answers. Sorry that I wasn't more specific in my initial post. The 500 $ are only for the camera. Filters are already set up. I have to measure fluorescence of moving particles with at least 20 samples per second (20 fps). Furthermore the sensor should be applicable for a broader spectrum. Right now I only have to detect one fluorophore. Besides that I basically don't have any constraints.
The moving particles are in a tube with fixed wall thickness. These particles are only moving in one direction and have a constant speed. So it's fine that I only measure the fluorescence directly in front of my sensor. I have to detect their presence/absence. I am triggering the fluorescence by illuminating the particles with light from a LED. I want to place my sensor perpendicular to the light source.

John Griessen schrieb am Montag, 23. November 2020 um 20:08:06 UTC+1:
On 11/23/20 5:46 AM, 'Charles Maldonado' via DIYbio wrote:
> Hi all,
>
> I am developing a DIY detection sytem for fluorescence. I want to do the actual detection with a camera, but right now I am
> struggling a little bit with the selection of this camera There are so many cameras available and I don't know, which one of them
> will allow me to detect fluorescence. I guess, I need operation in low-light conditions and a high SNR. But aside from that, I
> don't know, which minimal specs I need...
> I just want to use it for detection, not for imaging.

Hi Charles,

I like Lisa's suggestion of a component very much if you are dealing with a zone of light. If you have a cell colony and want to
choose the brightest pixel out of a blob or growing cells, an image sensor (camera) would be good, otherwise if it makes a zone of
uniform light (maybe from a vial or cuvette) it can be lined up with the field of view of a sensor and get good repeatable results
when using a vial to hold "stuff" and get light out of one side of it. What kind of it are you dealing with?

Do you have a way to control where your fluorescing "thing/suspension/slide/dish" is in front of the camera/sensor? For instance
if you have a cell suspension in a particular vial with a certain wall thickness of glass you could calibrate that for a light
intensity and it wold work fine if the shape of it fits somewhere so it always aims a zone of light the same way at a sensor.

--
John Griessen
blog.kitmatic.com Albuquerque NM building lab gear for biologists

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Re: [DIYbio] Camera for fluorescence detection system

On 11/23/20 5:46 AM, 'Charles Maldonado' via DIYbio wrote:
> Hi all,
>
> I am developing a DIY detection sytem for fluorescence. I want to do the actual detection with a camera, but right now I am
> struggling a little bit with the selection of this camera There are so many cameras available and I don't know, which one of them
> will allow me to detect fluorescence. I guess, I need operation in low-light conditions and a high SNR. But aside from that, I
> don't know, which minimal specs I need...
> I just want to use it for detection, not for imaging.

Hi Charles,

I like Lisa's suggestion of a component very much if you are dealing with a zone of light. If you have a cell colony and want to
choose the brightest pixel out of a blob or growing cells, an image sensor (camera) would be good, otherwise if it makes a zone of
uniform light (maybe from a vial or cuvette) it can be lined up with the field of view of a sensor and get good repeatable results
when using a vial to hold "stuff" and get light out of one side of it. What kind of it are you dealing with?

Do you have a way to control where your fluorescing "thing/suspension/slide/dish" is in front of the camera/sensor? For instance
if you have a cell suspension in a particular vial with a certain wall thickness of glass you could calibrate that for a light
intensity and it wold work fine if the shape of it fits somewhere so it always aims a zone of light the same way at a sensor.

--
John Griessen
blog.kitmatic.com Albuquerque NM building lab gear for biologists

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Re: [DIYbio] Camera for fluorescence detection system

do you have a diagram of your set up. 
BTW, cell phones work very well, you can set up exposure times, etc. 

On Mon, Nov 23, 2020 at 10:10 AM 'Charles Maldonado' via DIYbio <diybio@googlegroups.com> wrote:

Hi all,

I am developing a DIY detection sytem for fluorescence. I want to do the actual detection with a camera, but right now I am struggling a little bit with the selection of this camera There are so many cameras available and I don't know, which one of them will allow me to detect fluorescence. I guess, I need operation in low-light conditions and a high SNR. But aside from that, I don't know, which minimal specs I need...
I just want to use it for detection, not for imaging.
Could you help me please? My max budget is around 500 USD. But the cheaper, the better :D
Thanks!

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Re: [DIYbio] Camera for fluorescence detection system

Hi Charles,

if you only want to do detection, maybe something like the TSL235R would be an option for you - it's cheap, and it can detect very low levels of light. I've used it to quantify fluorescence from DNA dyes like SYBR Green in microliter volumes.

Kind regards,
Lisa

On 23. Nov 2020, at 19:10, 'Charles Maldonado' via DIYbio <diybio@googlegroups.com> wrote:


Hi all,

I am developing a DIY detection sytem for fluorescence. I want to do the actual detection with a camera, but right now I am struggling a little bit with the selection of this camera There are so many cameras available and I don't know, which one of them will allow me to detect fluorescence. I guess, I need operation in low-light conditions and a high SNR. But aside from that, I don't know, which minimal specs I need...
I just want to use it for detection, not for imaging.
Could you help me please? My max budget is around 500 USD. But the cheaper, the better :D
Thanks!

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Re: [DIYbio] Camera for fluorescence detection system

Hi Charles,


Let's narrow this down, do you have any constraints besides $500 and fluorescence?  Exposure time, weight, ISO sensitivity, filter cost?  A raspberry pi camera comes in 5mp ($8.50), 8mp ($25) and 12.3mp ($50).  How are you illuminating the sample? 


Best,
James


On Nov 23, 2020, at 6:46 AM, 'Charles Maldonado' via DIYbio <diybio@googlegroups.com> wrote:


Hi all,

I am developing a DIY detection sytem for fluorescence. I want to do the actual detection with a camera, but right now I am struggling a little bit with the selection of this camera There are so many cameras available and I don't know, which one of them will allow me to detect fluorescence. I guess, I need operation in low-light conditions and a high SNR. But aside from that, I don't know, which minimal specs I need...
I just want to use it for detection, not for imaging.
Could you help me please? My max budget is around 500 USD. But the cheaper, the better :D
Thanks!

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[DIYbio] Camera for fluorescence detection system


Hi all,

I am developing a DIY detection sytem for fluorescence. I want to do the actual detection with a camera, but right now I am struggling a little bit with the selection of this camera There are so many cameras available and I don't know, which one of them will allow me to detect fluorescence. I guess, I need operation in low-light conditions and a high SNR. But aside from that, I don't know, which minimal specs I need...
I just want to use it for detection, not for imaging.
Could you help me please? My max budget is around 500 USD. But the cheaper, the better :D
Thanks!

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Re: [DIYbio] 3D bioprinting

Hey Kristina,
   To add to the list, you could reach out to https://www.aspectbiosystems.com/ on Linkedin.

Thanks,
Sri

On Thu, Nov 19, 2020 at 12:50 PM S James Parsons Jr <sjamesparsonsjr@gmail.com> wrote:
Hi Kristina,

I would recommend reaching out to https://www.allevi3d.com/, or https://sunpbiotech.com/ 




On Nov 19, 2020, at 10:23 AM, Kristina Girčytė <kristinagir@gmail.com> wrote:

Hi,

I am a biologist. Now I am student from European Commission media academy project based in Lithuania (Europe). I am with my team creating a science promotion episode about 3D biotechnology use in medicine. The episode might be published on TV. I am read more some articles about 3D printing projects skin and organs and I am very interested in 3D bioprinting systems how help in medicine. I am looking for an interlocutor or consultant. Could you advise us somebody who would like to give us an interview about this topic?

 Sincerely,

Kristina Girčytė 

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Re: [DIYbio] 3D bioprinting

Hi Kristina,


I would recommend reaching out to https://www.allevi3d.com/, or https://sunpbiotech.com/ 




On Nov 19, 2020, at 10:23 AM, Kristina Girčytė <kristinagir@gmail.com> wrote:

Hi,

I am a biologist. Now I am student from European Commission media academy project based in Lithuania (Europe). I am with my team creating a science promotion episode about 3D biotechnology use in medicine. The episode might be published on TV. I am read more some articles about 3D printing projects skin and organs and I am very interested in 3D bioprinting systems how help in medicine. I am looking for an interlocutor or consultant. Could you advise us somebody who would like to give us an interview about this topic?

 Sincerely,

Kristina Girčytė 

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[DIYbio] 3D bioprinting

Hi,

I am a biologist. Now I am student from European Commission media academy project based in Lithuania (Europe). I am with my team creating a science promotion episode about 3D biotechnology use in medicine. The episode might be published on TV. I am read more some articles about 3D printing projects skin and organs and I am very interested in 3D bioprinting systems how help in medicine. I am looking for an interlocutor or consultant. Could you advise us somebody who would like to give us an interview about this topic?


 Sincerely,


Kristina Girčytė 

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[DIYbio] THE OPEN BIOECONOMY LAB

https://openbioeconomy.org/

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[DIYbio] Talk on ethics in DIYbio/CommunityBio spaces

Hi folks!

I'm giving a talk at UNCC on Thursday at 12pm Eastern about the ethics work many on this thread participated in at last year's Global Community Bio Summit! I'll discuss the way we created the ethics workshops, the ways the community collaborated to develop a list of shared ethics norms (document 1.0), and how that list is meant to be used as a living document and a tool to engage with ethics across DIYbio and other independent research contexts. 

Hope to see some of you there!
Cheers, 
Alex Pearlman

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[DIYbio] Pichia pastoris

Anybody here working with Pichia? We want to try using that organism to play around in the open lab but... the commecial strains seem very expensive. Does anyone have a standard lab strain they would be willing to share (of course all shipping costs and a handling fee will be paid)? 





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[DIYbio] Re: RADVAC - (homebrew) Corona Vaccine



I believe GenScript is a reliable source.


https://www.genscript.com/peptide-services.html?src=service

Sigma is great for the other dry ingredients.

Brian

El sábado, 31 de octubre de 2020 a la(s) 17:06:53 UTC+1, deacon.d...@gmail.com escribió:
Yes, looking into it and working on sourcing ingredients for it.  It's difficult to find a reliable peptide supplier because there are many scam operations that will send you an empty tube with a nice label instead of a real product. Chitosan is ~$50 from Sigma.

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Re: [DIYbio] RADVAC - (homebrew) Corona Vaccine


I became fascinated with RaDVaC as soon as I learned about it in July. I studied the white paper, read most of the references carefully, and decided to take, and make, the vaccine. In fact, I've now created a "mobile RaDVaC lab" that fits in a small suitcase, and have traveled with it to help show people how to make the vaccine. (Then I just leave the equipment with them, and buy more. It's a few hundred dollars for a complete set-up.)

I think the project is brilliant.

http://infinitefaculty.org/RaDVaC/Decision_tree.html

Brian

https://radvac.org/

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