FINAL CALL: NEW ABRF Study#3 Light Microscopy Research Group Study

[Claire Brown]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****



Hello All,



The ABRF Light Microscopy Research Group (LMRG) has spent considerable time designing, testing and refining the sample type, preparation and imaging protocols for our latest study. The new study will focus on metrics for spherical aberration, sensitivity and signal-to-noise for 3D imaging using a microsphere sample in a tissue like environment. The study overview is below. If you register for the study you will receive an imaging protocol and a sample - which MUST be imaged within one week of its arrival - NO ADDITIONAL SAMPLES WILL BE SENT - so we are asking you to identify an ideal time frame to receive the sample and collect the data.



WE HAVE EXTENDED THE DEADLINE TO MONDAY NOVEMBER 10TH, 2014 IF YOU ARE STILL INTERESTED IN SIGNING UP FOR THE STUDY.



https://www.surveymonkey.com/r/LMRG_Study_3



FYI aside from a pre-meeting image processing and analysis workshop, a keynote microscopy talk (John Condeelis - Albert Einstein) and a full three day microscopy track the ABRF 2015 meeting in St. Louis, MO March 28-31 will feature a session on microscope standards! For more info see conf.abrf.org



If you have any questions or concerns feel free to email me.



Sincerely,



Claire





ABRF-LMRG Study Overview



Introduction: The third study of the Association of Biomolecular Resource Facilities (ABRF) Light Microscopy Research Group (LMRG) is aimed at creating a 3D biologically relevant test slide and imaging protocol to test for 1) system resolution and distortions in 2D and 3D, 2) the dependence of Intensity quantification and image signal-to-noise of the microscope on imaging depth and 3) the dependence of the microscope sensitivity on imaging depth.



Specimen Detail: Fluorescence microspheres (Life Technologies) imbedded in a 120 µm-thick layer of CyGel (BioStatus, UK, Cat# Cy10500) with a refractive index of 1.36 closely match biological tissue. Double-sided adhesive 18 mm square spacers with a well (9 mm diameter, 120 µm deep) were used for the sample preparation (Electron Microscopy Sciences, Cat# 70327-8s).



---------------------------------------------



Imaging Conditions: The microsphere samples should be imaged from the coverslip up to 100 µm into the sample. The sample region should include a good selection of 5-10 of each of the different microspheres listed above. A z-stack of images should be collected as per the attached protocols with a minimal x-y and z resolution 0.35 µm. This will result in a data set with approximately 300 images having all the information required to test system resolution, quantification, the signal-to-noise ratio (S/N), and sensitivity.



Metrics: Image stacks will be sent to the LMRG for image analysis, consolidation of the data and interpretation of the results. Briefly, here are the metrics that will be measured.



1)     System Resolution



a.      2D Resolution: PSF FWHM along the x-y axis for 5 microspheres at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.



b.      3D Resolution: PSF FWHM along the x-z or y-z axis for 5 microspheres at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.



c.      Visual Inspection of PSF Shape: Visual inspection for aberrations and scoring of PSF shape along the x-z and y-z axes.



2)     Quantification and S/N



a.      Quantify Relative Microsphere Intensities: Measure 5 microsphere pair intensity ratios at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.



b.      Measurement of S/N ratio: S/N ratio for microsphere intensity of 5 microspheres at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.



3)     Sensitivity



a.     Microsphere Intensity: Compare the intensity of 5 microspheres at depths of 0-25 *m, 25-50 *m, 50-75 *m, 75-100 *m.

Sincerely,

Claire

*******************************************************************
Association of Biomolecular Resource Facilities (ABRF) Annual Meeting
March 28-31, 2015, St. Louis, MO, conf.abrf.org

Canadian Cytometry and Microscopy (CCMA) Symposium - Technologies to Treatments
June 18-20, 2015, Toronto, ON, www.cytometry.ca<http://www.cytometry.ca>

[George McNamara]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Claire, the Next Gen Sequencers are way ahead of the LMRG

http://www.youtube.com/watch?v=rZFcHlXL7nk&feature=youtu.be



On 11/4/2014 2:23 PM, Claire Brown, Dr. wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
>
>
> Hello All,
>
>
>
> The ABRF Light Microscopy Research Group (LMRG) has spent considerable time designing, testing and refining the sample type, preparation and imaging protocols for our latest study. The new study will focus on metrics for spherical aberration, sensitivity and signal-to-noise for 3D imaging using a microsphere sample in a tissue like environment. The study overview is below. If you register for the study you will receive an imaging protocol and a sample - which MUST be imaged within one week of its arrival - NO ADDITIONAL SAMPLES WILL BE SENT - so we are asking you to identify an ideal time frame to receive the sample and collect the data.
>
>
>
> WE HAVE EXTENDED THE DEADLINE TO MONDAY NOVEMBER 10TH, 2014 IF YOU ARE STILL INTERESTED IN SIGNING UP FOR THE STUDY.
>
>
>
> https://www.surveymonkey.com/r/LMRG_Study_3
>
>
>
> FYI aside from a pre-meeting image processing and analysis workshop, a keynote microscopy talk (John Condeelis - Albert Einstein) and a full three day microscopy track the ABRF 2015 meeting in St. Louis, MO March 28-31 will feature a session on microscope standards! For more info see conf.abrf.org
>
>
>
> If you have any questions or concerns feel free to email me.
>
>
>
> Sincerely,
>
>
>
> Claire
>
>
>
>
>
> ABRF-LMRG Study Overview
>
>
>
> Introduction: The third study of the Association of Biomolecular Resource Facilities (ABRF) Light Microscopy Research Group (LMRG) is aimed at creating a 3D biologically relevant test slide and imaging protocol to test for 1) system resolution and distortions in 2D and 3D, 2) the dependence of Intensity quantification and image signal-to-noise of the microscope on imaging depth and 3) the dependence of the microscope sensitivity on imaging depth.
>
>
>
> Specimen Detail: Fluorescence microspheres (Life Technologies) imbedded in a 120 µm-thick layer of CyGel (BioStatus, UK, Cat# Cy10500) with a refractive index of 1.36 closely match biological tissue. Double-sided adhesive 18 mm square spacers with a well (9 mm diameter, 120 µm deep) were used for the sample preparation (Electron Microscopy Sciences, Cat# 70327-8s).
>
>
>
> ---------------------------------------------
>
>
>
> Imaging Conditions: The microsphere samples should be imaged from the coverslip up to 100 µm into the sample. The sample region should include a good selection of 5-10 of each of the different microspheres listed above. A z-stack of images should be collected as per the attached protocols with a minimal x-y and z resolution 0.35 µm. This will result in a data set with approximately 300 images having all the information required to test system resolution, quantification, the signal-to-noise ratio (S/N), and sensitivity.
>
>
>
> Metrics: Image stacks will be sent to the LMRG for image analysis, consolidation of the data and interpretation of the results. Briefly, here are the metrics that will be measured.
>
>
>
> 1)     System Resolution
>
>
>
> a.      2D Resolution: PSF FWHM along the x-y axis for 5 microspheres at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.
>
>
>
> b.      3D Resolution: PSF FWHM along the x-z or y-z axis for 5 microspheres at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.
>
>
>
> c.      Visual Inspection of PSF Shape: Visual inspection for aberrations and scoring of PSF shape along the x-z and y-z axes.
>
>
>
> 2)     Quantification and S/N
>
>
>
> a.      Quantify Relative Microsphere Intensities: Measure 5 microsphere pair intensity ratios at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.
>
>
>
> b.      Measurement of S/N ratio: S/N ratio for microsphere intensity of 5 microspheres at each depth of 0-25 µm, 25-50 µm, 50-75 µm, 75-100 µm.
>
>
>
> 3)     Sensitivity
>
>
>
> a.     Microsphere Intensity: Compare the intensity of 5 microspheres at depths of 0-25 *m, 25-50 *m, 50-75 *m, 75-100 *m.
>
> Sincerely,
>
> Claire
>
> *******************************************************************
> Association of Biomolecular Resource Facilities (ABRF) Annual Meeting
> March 28-31, 2015, St. Louis, MO, conf.abrf.org
>
> Canadian Cytometry and Microscopy (CCMA) Symposium - Technologies to Treatments
> June 18-20, 2015, Toronto, ON, www.cytometry.ca<http://www.cytometry.ca>
>
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42