Difference between revisions of "Weekly Updates"

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(Created page with "== Week 03/14 – 03/18 == === This Week === - Defined a modified equipment list with the help of Uli and Jeff at the Danuser lab (simplified design without TIRF and a single ...")
 
(→‎Week 03/14 – 03/18)
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- There is a delay on the planned time for part ordering, which has to be addressed next week or shipping and processing time might interfere with the project execution
 
- There is a delay on the planned time for part ordering, which has to be addressed next week or shipping and processing time might interfere with the project execution
 +
 +
== Week 03/21 – 03/25 ==
 +
 +
=== This Week ===
 +
- Additional reading was done on the part selection software
 +
 +
- The options for lasers were evaluated. In particular, OEM seems to be the best option based on their price to quality relation. The particular wavelength will depend on the dye selection
 +
 +
- Research was done into the image processing software, and the best option seems to be adapting the QuickPALM code available in open source to our needs
 +
 +
- Jeff and Uli gave more feedback on the project, clarifying that the image processing can probably be done with a simple Gaussian fit, so research was put into that
 +
 +
=== Next Week ===
 +
 +
- Try and finish the research for part selection
 +
 +
- Get the best photon budget possible for part selection
 +
 +
- Continue work in image processing, in particular adapting the QuickPALM to our needs
 +
 +
=== Risks and Issues ===
 +
 +
- The part selection process is taking a lot longer than expected, which could result in delays in the schedule
 +
 +
- The reading required for the photon budget seems to be considerable, so again that may affect the proposed schedule
 +
 +
- Reverse engineering and adapting the QuickPALM code might be more complicated than just programming our own code
 +
 +
== Week 03/28 – 04/01 ==
 +
 +
=== This Week ===
 +
 +
- Continued research on parts and photon budget, taking a lot of information from the Olympus resource website. The light path from laser to sample is complete
 +
 +
- Research was put into dSTORM, and determining if it is a viable option for our project, both in terms of equipment and software
 +
 +
- Quotes were obtained for the Andor and Hamamatsu cameras. The latter seems to be the best option (Orca Flash 2.8)
 +
 +
=== Next Week ===
 +
 +
- Again attempt to finish the photon budget, addressing the sources of noise and the path from sample to camera
 +
 +
- Determine if dSTORM is viable, so that one laser can be used
 +
 +
=== Risks and Issues ===
 +
 +
- We are falling behind schedule in both the part selection and the image processing, the amount of information necessary keeps increasing
 +
 +
- If dSTORM is selected, there is a risk of not having enough photons to perform the experiments, even at long integration times
 +
 +
- The performance of the Orca Flash 2.8 is a lot lower than the EM-CCD and Neo-sCMOS cameras, so there is a chance there is no way of neglecting the high-price cameras
 +
 +
== Week 04/04 – 04/08 ==
 +
 +
=== This Week ===
 +
 +
- Finished the sample to camera photon budget, tailored for single particle detection based on Gaussian fits
 +
 +
- The dye selection seems to point to ATTO 680, since it is an order of magnitude faster than Cy5 for dSTORM, even when Cy5 is complexed
 +
 +
- Evaluated different camera and dye options using the photon budget calculations
 +
 +
=== Next Week ===
 +
 +
- Order the laser and setup the demo for the camera
 +
 +
- Fully understand the QuickPALM code
 +
 +
- Adapt the existing microscope frame for addition of the new laser and the new camera
 +
 +
=== Risks and Issues ===
 +
 +
- The election of dSTORM is a risky choice, since there might not be enough photons to collect and the system might be too slow
 +
 +
- The availability of the ATTO 680 dye might be less ideal than Cy5

Revision as of 18:08, 12 April 2011

Week 03/14 – 03/18

This Week

- Defined a modified equipment list with the help of Uli and Jeff at the Danuser lab (simplified design without TIRF and a single laser)

- Research was made on the best choices for lasers, cameras and objectives

- The microscope at station 3 was approved for use with the e-STORM project, with minor modifications depending on the specific parts acquired

Next Week

- A final equipment list will be compiled and quotes will be obtained

- Ideally, the equipment will be ordered

- Work will start with the image analysis programming, including the analysis of code obtained from the Danuser lab plus literature reading

Risks and Issues

- The adoption of the microscope frame at station 3 might be premature depending on the final parts and design we acquire

- There might be a fair amount of experimentation with the setup since we are using the most minimalist approach possible

- There is a delay on the planned time for part ordering, which has to be addressed next week or shipping and processing time might interfere with the project execution

Week 03/21 – 03/25

This Week

- Additional reading was done on the part selection software

- The options for lasers were evaluated. In particular, OEM seems to be the best option based on their price to quality relation. The particular wavelength will depend on the dye selection

- Research was done into the image processing software, and the best option seems to be adapting the QuickPALM code available in open source to our needs

- Jeff and Uli gave more feedback on the project, clarifying that the image processing can probably be done with a simple Gaussian fit, so research was put into that

Next Week

- Try and finish the research for part selection

- Get the best photon budget possible for part selection

- Continue work in image processing, in particular adapting the QuickPALM to our needs

Risks and Issues

- The part selection process is taking a lot longer than expected, which could result in delays in the schedule

- The reading required for the photon budget seems to be considerable, so again that may affect the proposed schedule

- Reverse engineering and adapting the QuickPALM code might be more complicated than just programming our own code

Week 03/28 – 04/01

This Week

- Continued research on parts and photon budget, taking a lot of information from the Olympus resource website. The light path from laser to sample is complete

- Research was put into dSTORM, and determining if it is a viable option for our project, both in terms of equipment and software

- Quotes were obtained for the Andor and Hamamatsu cameras. The latter seems to be the best option (Orca Flash 2.8)

Next Week

- Again attempt to finish the photon budget, addressing the sources of noise and the path from sample to camera

- Determine if dSTORM is viable, so that one laser can be used

Risks and Issues

- We are falling behind schedule in both the part selection and the image processing, the amount of information necessary keeps increasing

- If dSTORM is selected, there is a risk of not having enough photons to perform the experiments, even at long integration times

- The performance of the Orca Flash 2.8 is a lot lower than the EM-CCD and Neo-sCMOS cameras, so there is a chance there is no way of neglecting the high-price cameras

Week 04/04 – 04/08

This Week

- Finished the sample to camera photon budget, tailored for single particle detection based on Gaussian fits

- The dye selection seems to point to ATTO 680, since it is an order of magnitude faster than Cy5 for dSTORM, even when Cy5 is complexed

- Evaluated different camera and dye options using the photon budget calculations

Next Week

- Order the laser and setup the demo for the camera

- Fully understand the QuickPALM code

- Adapt the existing microscope frame for addition of the new laser and the new camera

Risks and Issues

- The election of dSTORM is a risky choice, since there might not be enough photons to collect and the system might be too slow

- The availability of the ATTO 680 dye might be less ideal than Cy5

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