Position Opening ? Technical Support Specialist Bitplane Inc.

[Michael C. Wussow]

Position Opening ? Technical Support Specialist

Further information on this position can be found here: http://www.bitplane.com/go/bitplane/jobs

Bitplane AG is a world leader in 3-D and 4-D imaging software for the Life Sciences Industry.  Its North American operations (headquartered in Saint Paul, MN) is seeking qualified candidates for the position of Technical Support Specialist.  We are looking for a candidate with strong computer skills and at least one year of hands-on working experience using a confocal or similar 3D advanced light microscope. Applicants must be excited by the latest computer and microscope technologies and have a well-founded biological knowledge base. Candidates must enjoy the challenges of working in a dynamic market where products, research technologies, and demands are continually evolving.

The requirements for this position are:

• You have worked with a confocal microscope (or other 3D light microscope) studying biological samples.
• You are a self-motivated individual who is able to work independently and capable of managing multiple projects.
• In-depth knowledge of and proficiency with Microsoft Windows
• Technical knowledge of PC hardware, subsystems, peripheral and networking equipment
• Strong written and verbal communication skills in English with an adequate technical and biological vocabulary, and natural ability to adapt communication style to interface with clients in a wide range of positions and experience levels
• Strong interpersonal skills and excellent customer services ethic
• You have had a prior position where you could demonstrate your problem solving skills.
• You are already located in the eastern half of the US, or willing to relocate there.   Some additional geographic details to be discussed, but specific city and state of residence is very flexible overall.           

Desirable, but not required experience:

• Prior experience using Imaris, or other software with comparable features.
• Proficiency with Mac OSX
• Basic knowledge in Matlab

The duties of this position include:

• Technical support for 3D Imaging analysis software for microscopy.
• Pro-active communication with customers via telephone and email to ensure that you understand the issue and they understand the resolution.
• You will combine product understanding, technical skills, and biological know-how to investigate problems at hand and to provide an optimal solution to the customer.
• You will also assist our sales-team with preparing customer data for a sales presentation.
• Reporting and cataloguing software problems, bugs and feature requests; including testing of pre-release (alpha/beta) versions of the software
• This job requires you to perform on-site customer trainings, represent Bitplane at courses & meetings, and involves approximately 10-20% of time travelling.

Benefits include a base salary, 401K plan, healthcare, and vacation. Representative will work out of a home office. In addition, we offer a fun team to work with as well as a truly international environment that provides the resources required to grow. Bitplane will fully cover your expenses for equipment, internet access, telephone, and travel.

If you are interested in joining this team of professionals and your qualifications meet these requirements, send us your resume and cover letter for consideration.  Please include your salary history and/or salary requirements.  Compensation will be commensurate with relevant experience.

Respond to: 

Michael C. Wussow
VP & General Manager
Bitplane Inc.
e-mail: [hidden email]facsimile: 866-691-9112

[confocalservice]

Hi

 

Is this based in USA?

thanks

2009/10/20 Michael C Wussow <[hidden email]>

Position Opening ? Technical Support Specialist

Further information on this position can be found here: http://www.bitplane.com/go/bitplane/jobs

Bitplane AG is a world leader in 3-D and 4-D imaging software for the Life Sciences Industry.  Its North American operations (headquartered in Saint Paul, MN) is seeking qualified candidates for the position of Technical Support Specialist.  We are looking for a candidate with strong computer skills and at least one year of hands-on working experience using a confocal or similar 3D advanced light microscope. Applicants must be excited by the latest computer and microscope technologies and have a well-founded biological knowledge base. Candidates must enjoy the challenges of working in a dynamic market where products, research technologies, and demands are continually evolving.

The requirements for this position are:

• You have worked with a confocal microscope (or other 3D light microscope) studying biological samples.
• You are a self-motivated individual who is able to work independently and capable of managing multiple projects.
• In-depth knowledge of and proficiency with Microsoft Windows
• Technical knowledge of PC hardware, subsystems, peripheral and networking equipment
• Strong written and verbal communication skills in English with an adequate technical and biological vocabulary, and natural ability to adapt communication style to interface with clients in a wide range of positions and experience levels
• Strong interpersonal skills and excellent customer services ethic
• You have had a prior position where you could demonstrate your problem solving skills.
• You are already located in the eastern half of the US, or willing to relocate there.   Some additional geographic details to be discussed, but specific city and state of residence is very flexible overall.           

Desirable, but not required experience:

• Prior experience using Imaris, or other software with comparable features.
• Proficiency with Mac OSX
• Basic knowledge in Matlab

The duties of this position include:

• Technical support for 3D Imaging analysis software for microscopy.
• Pro-active communication with customers via telephone and email to ensure that you understand the issue and they understand the resolution.
• You will combine product understanding, technical skills, and biological know-how to investigate problems at hand and to provide an optimal solution to the customer.
• You will also assist our sales-team with preparing customer data for a sales presentation.
• Reporting and cataloguing software problems, bugs and feature requests; including testing of pre-release (alpha/beta) versions of the software
• This job requires you to perform on-site customer trainings, represent Bitplane at courses & meetings, and involves approximately 10-20% of time travelling.

Benefits include a base salary, 401K plan, healthcare, and vacation. Representative will work out of a home office. In addition, we offer a fun team to work with as well as a truly international environment that provides the resources required to grow. Bitplane will fully cover your expenses for equipment, internet access, telephone, and travel.

If you are interested in joining this team of professionals and your qualifications meet these requirements, send us your resume and cover letter for consideration.  Please include your salary history and/or salary requirements.  Compensation will be commensurate with relevant experience.

Respond to: 

Michael C. Wussow
VP & General Manager
Bitplane Inc.
e-mail: [hidden email]facsimile: 866-691-9112

[John Oreopoulos]

I have some confocal z-stacks of cells expressing a fluorescent protein and I've encountered something I haven't had to deal with before. I'm wondering what is the best way to subtract the background signal from a z-stack like this. My problem is that the background is different for each z-step, peaking a the z-height corresponding to the bottom of the cells that are in contact with the substrate - supposedly since this is the height where you have the most reflection of the excitation light from the substrate itself backwards to the detector. 

Which is better? Should I subtract the maximum background level of the substrate slice from all slices or subtract the background of each individual slice from themselves only? Or I could subtract the average background over all slices from each slice instead of the maximum value at the substrate slice. Alternatively, should I create the z-projection and subtract the background of the z-projection image?

Thanks for anyone who can clear this up for me.

John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging

[mmodel]

John,

 

If it’s just for display maybe it’s better not to subtract the background at all because this may create false impression that your images are cleaner than they really are. But if you are trying to do quantify intensity over the background I think correcting each plane individually makes more sense. For the maximum intensity projection you may just skip the plane where the reflection is strong, this plane may not carry much useful information anyway.

 

Mike

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
Sent: Wednesday, October 21, 2009 12:36 PM
To: [hidden email]
Subject: Background subtraction from a 3D confocal z-stack

 

I have some confocal z-stacks of cells expressing a fluorescent protein and I've encountered something I haven't had to deal with before. I'm wondering what is the best way to subtract the background signal from a z-stack like this. My problem is that the background is different for each z-step, peaking a the z-height corresponding to the bottom of the cells that are in contact with the substrate - supposedly since this is the height where you have the most reflection of the excitation light from the substrate itself backwards to the detector. 

 

Which is better? Should I subtract the maximum background level of the substrate slice from all slices or subtract the background of each individual slice from themselves only? Or I could subtract the average background over all slices from each slice instead of the maximum value at the substrate slice. Alternatively, should I create the z-projection and subtract the background of the z-projection image?

 

Thanks for anyone who can clear this up for me.

 

John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging

 

[John Oreopoulos]

Yes, this is a good point. I should have specified that I'm trying to do some quantitative colocalization and FRET analysis, not just visual display, so I think the subtraction is necessary.

John

On 21-Oct-09, at 12:42 PM, MODEL, MICHAEL wrote:

John,

 

If it’s just for display maybe it’s better not to subtract the background at all because this may create false impression that your images are cleaner than they really are. But if you are trying to do quantify intensity over the background I think correcting each plane individually makes more sense. For the maximum intensity projection you may just skip the plane where the reflection is strong, this plane may not carry much useful information anyway.

 

Mike

 

From: Confocal Microscopy List [[hidden email]] On Behalf Of John Oreopoulos
Sent: Wednesday, October 21, 2009 12:36 PM
To: [hidden email]
Subject: Background subtraction from a 3D confocal z-stack

 

I have some confocal z-stacks of cells expressing a fluorescent protein and I've encountered something I haven't had to deal with before. I'm wondering what is the best way to subtract the background signal from a z-stack like this. My problem is that the background is different for each z-step, peaking a the z-height corresponding to the bottom of the cells that are in contact with the substrate - supposedly since this is the height where you have the most reflection of the excitation light from the substrate itself backwards to the detector. 

 

Which is better? Should I subtract the maximum background level of the substrate slice from all slices or subtract the background of each individual slice from themselves only? Or I could subtract the average background over all slices from each slice instead of the maximum value at the substrate slice. Alternatively, should I create the z-projection and subtract the background of the z-projection image?

 

Thanks for anyone who can clear this up for me.

 

John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging

 

[Julio Vazquez]

-

All of Michael's suggestions make sense. However, you should also consider the specifics of your data and of your experiment. For example, we had someone recently who was looking at labeled cells. There was a high level of background in the medium around the cells (probably because of some chemicals in the medium), but the cells themselves were quite dark (because they excluded whatever chemical was responsible for the background fluorescence). In this case, you can not simply subtract an average background value, because then the specific signal in your cells gets underestimated. In that case, you probably need to get an estimate of the real intracellular background to perform accurate colocalization and/or FRET calculations. We encounter this problem in high content screens where the algorithm allows us to define a radius around the objects (cells) to determine the background to be subtracted. For the same sample, the results of the background subtraction will be extremely dependent on cell density and on a judicious choice of that radius. If cells are sparse, a good estimate of the background will be achieved by using a radius several times larger than the cells. However, if cells are tightly packed, the region chosen to calculate the background will contain cells (i.e. specific signal), and the background values will be overestimated. Hence, for precise calculations, I would often measure the background manually in representative "background" regions inside the cells. 

--

Julio Vazquez, 

Fred Hutchinson Cancer Research Center

Seattle, WA 98109-1024

http://www.fhcrc.org/ 

==

On Oct 21, 2009, at 9:49 AM, John Oreopoulos wrote:

Yes, this is a good point. I should have specified that I'm trying to do some quantitative colocalization and FRET analysis, not just visual display, so I think the subtraction is necessary.

John

On 21-Oct-09, at 12:42 PM, MODEL, MICHAEL wrote:

John,

 

If it’s just for display maybe it’s better not to subtract the background at all because this may create false impression that your images are cleaner than they really are. But if you are trying to do quantify intensity over the background I think correcting each plane individually makes more sense. For the maximum intensity projection you may just skip the plane where the reflection is strong, this plane may not carry much useful information anyway.

 

Mike

 

From: Confocal Microscopy List [[hidden email]] On Behalf Of John Oreopoulos
Sent: Wednesday, October 21, 2009 12:36 PM
To: [hidden email]
Subject: Background subtraction from a 3D confocal z-stack

 

I have some confocal z-stacks of cells expressing a fluorescent protein and I've encountered something I haven't had to deal with before. I'm wondering what is the best way to subtract the background signal from a z-stack like this. My problem is that the background is different for each z-step, peaking a the z-height corresponding to the bottom of the cells that are in contact with the substrate - supposedly since this is the height where you have the most reflection of the excitation light from the substrate itself backwards to the detector. 

 

Which is better? Should I subtract the maximum background level of the substrate slice from all slices or subtract the background of each individual slice from themselves only? Or I could subtract the average background over all slices from each slice instead of the maximum value at the substrate slice. Alternatively, should I create the z-projection and subtract the background of the z-projection image?

 

Thanks for anyone who can clear this up for me.

 

John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging

 

[Mark Cannell]

Hi John

Obviously, subtracting a single number is not correct.  If you know what
the background is due to you can subtract a model for its behavior (e.g.
if it is reflection it should follow the z-response of the microscope) .
If you have no knowledge of the backgound behavior you can directly
measure the background in a region where you _know_ there is no signal
-this could be another z-stack in a region without stained cells. If you
have a source of "non specific" signal in  the specimen (e.g. cell
autofluorescence),  you have a bigger problem as that can't be simply
subtracted -it's actually data. This will increase the number of
measurements needed to detect a difference between control and treated
cells for example.

If it's a reflection problem can't you fix it (e.g better filter
combinations and/or a polarizer)?

My 2c

Cheers Mark Cannell





John Oreopoulos wrote:

> I have some confocal z-stacks of cells expressing a fluorescent
> protein and I've encountered something I haven't had to deal with
> before. I'm wondering what is the best way to subtract the background
> signal from a z-stack like this. My problem is that the background is
> different for each z-step, peaking a the z-height corresponding to the
> bottom of the cells that are in contact with the substrate -
> supposedly since this is the height where you have the most reflection
> of the excitation light from the substrate itself backwards to the
> detector.
>
> Which is better? Should I subtract the maximum background level of the
> substrate slice from all slices or subtract the background of each
> individual slice from themselves only? Or I could subtract the average
> background over all slices from each slice instead of the maximum
> value at the substrate slice. Alternatively, should I create the
> z-projection and subtract the background of the z-projection image?
>
> Thanks for anyone who can clear this up for me.
>
>
> John Oreopoulos, BSc,
>
> PhD Candidate
>
> University of Toronto
>
> Institute For Biomaterials and Biomedical Engineering
>
> Centre For Studies in Molecular Imaging
>
>

[John Oreopoulos]

I tried measuring the average background in a 90x90 pixel ROI where  
there are no cells for each z-slice (41 slices total). My images have  
been converted to 8-bit and if I plot the background signal in each  
ROI as a function of z-slice number, it has sort of a sharp poisson  
distribution shape with a peak of 81 counts at slice number seven and  
drops to a lower count value of 8 for the last twenty slices at the  
top of the stack. Slice seven also corresponds to the z-height that  
seems to match the bottom of the cells in contact with the glass  
coverslip as I mentioned before. I could try fitting a polynomial to  
this graph and then subtracting this trend from the image set. Is  
this what you mean by subtracting a model of the z-response of the  
microscope?

John

On 21-Oct-09, at 2:47 PM, Mark Cannell wrote:

> Hi John
>
> Obviously, subtracting a single number is not correct.  If you know  
> what the background is due to you can subtract a model for its  
> behavior (e.g. if it is reflection it should follow the z-response  
> of the microscope) . If you have no knowledge of the backgound  
> behavior you can directly measure the background in a region where  
> you _know_ there is no signal -this could be another z-stack in a  
> region without stained cells. If you have a source of "non  
> specific" signal in  the specimen (e.g. cell autofluorescence),  
> you have a bigger problem as that can't be simply subtracted -it's  
> actually data. This will increase the number of measurements needed  
> to detect a difference between control and treated cells for example.
>
> If it's a reflection problem can't you fix it (e.g better filter  
> combinations and/or a polarizer)?
>
> My 2c
>
> Cheers Mark Cannell
>
>
>
>
>
> John Oreopoulos wrote:
>> I have some confocal z-stacks of cells expressing a fluorescent  
>> protein and I've encountered something I haven't had to deal with  
>> before. I'm wondering what is the best way to subtract the  
>> background signal from a z-stack like this. My problem is that the  
>> background is different for each z-step, peaking a the z-height  
>> corresponding to the bottom of the cells that are in contact with  
>> the substrate - supposedly since this is the height where you have  
>> the most reflection of the excitation light from the substrate  
>> itself backwards to the detector.
>> Which is better? Should I subtract the maximum background level of  
>> the substrate slice from all slices or subtract the background of  
>> each individual slice from themselves only? Or I could subtract  
>> the average background over all slices from each slice instead of  
>> the maximum value at the substrate slice. Alternatively, should I  
>> create the z-projection and subtract the background of the z-
>> projection image?
>>
>> Thanks for anyone who can clear this up for me.
>>
>>
>> John Oreopoulos, BSc,
>>
>> PhD Candidate
>>
>> University of Toronto
>>
>> Institute For Biomaterials and Biomedical Engineering
>>
>> Centre For Studies in Molecular Imaging
>>
>>

[Mark Cannell]

Yes that would be a model. If the background is due to reflection it
should follow the z-response which may be better modeled by a Gaussian
(in this case you are missing a part of one side of it).  The constant
of 8 may be due to autofluorescence or stray light? Anyway, with a 90x90
ROI with no cells in it you would seem to have an accurate estimate of
background so I would use that for each slice.

Cheers

John Oreopoulos wrote:

> I tried measuring the average background in a 90x90 pixel ROI where
> there are no cells for each z-slice (41 slices total). My images have
> been converted to 8-bit and if I plot the background signal in each
> ROI as a function of z-slice number, it has sort of a sharp poisson
> distribution shape with a peak of 81 counts at slice number seven and
> drops to a lower count value of 8 for the last twenty slices at the
> top of the stack. Slice seven also corresponds to the z-height that
> seems to match the bottom of the cells in contact with the glass
> coverslip as I mentioned before. I could try fitting a polynomial to
> this graph and then subtracting this trend from the image set. Is this
> what you mean by subtracting a model of the z-response of the microscope?
>
> John
>
> On 21-Oct-09, at 2:47 PM, Mark Cannell wrote:
>
>> Hi John
>>
>> Obviously, subtracting a single number is not correct.  If you know
>> what the background is due to you can subtract a model for its
>> behavior (e.g. if it is reflection it should follow the z-response of
>> the microscope) . If you have no knowledge of the backgound behavior
>> you can directly measure the background in a region where you _know_
>> there is no signal -this could be another z-stack in a region without
>> stained cells. If you have a source of "non specific" signal in  the
>> specimen (e.g. cell autofluorescence),  you have a bigger problem as
>> that can't be simply subtracted -it's actually data. This will
>> increase the number of measurements needed to detect a difference
>> between control and treated cells for example.
>>
>> If it's a reflection problem can't you fix it (e.g better filter
>> combinations and/or a polarizer)?
>>
>> My 2c
>>
>> Cheers Mark Cannell
>>
>>
>>
>>
>>
>> John Oreopoulos wrote:
>>> I have some confocal z-stacks of cells expressing a fluorescent
>>> protein and I've encountered something I haven't had to deal with
>>> before. I'm wondering what is the best way to subtract the
>>> background signal from a z-stack like this. My problem is that the
>>> background is different for each z-step, peaking a the z-height
>>> corresponding to the bottom of the cells that are in contact with
>>> the substrate - supposedly since this is the height where you have
>>> the most reflection of the excitation light from the substrate
>>> itself backwards to the detector.
>>> Which is better? Should I subtract the maximum background level of
>>> the substrate slice from all slices or subtract the background of
>>> each individual slice from themselves only? Or I could subtract the
>>> average background over all slices from each slice instead of the
>>> maximum value at the substrate slice. Alternatively, should I create
>>> the z-projection and subtract the background of the z-projection image?
>>>
>>> Thanks for anyone who can clear this up for me.
>>>
>>>
>>> John Oreopoulos, BSc,
>>>
>>> PhD Candidate
>>>
>>> University of Toronto
>>>
>>> Institute For Biomaterials and Biomedical Engineering
>>>
>>> Centre For Studies in Molecular Imaging
>>>
>>>