مورد إلكتروني
High-density volumetric super-resolution microscopy
| العنوان: | High-density volumetric super-resolution microscopy |
|---|---|
| المؤلفون: | Daly, Sam, Ferreira Fernandes, João, Bruggeman, Ezra, Handa, Anoushka, Peters, Ruby, Benaissa, Sarah, Zhang, Boya, Beckwith, Joseph S., Sanders, Edward W., Sims, Ruth R., Klenerman, David, Davis, Simon J., O'Holleran, Kevin, Lee, Steven F. |
| سنة النشر: | 2023 |
| المجموعة: | Zenodo |
| مصطلحات موضوعية: | super-resolution microscopy, single molecule light field microscopy, single particle tracking |
| الوصف: | Overview Code and example data associated with 'High-density volumetric super-resolution microscopy' by Daly et al. including: 3D reconstruction code for single molecule light field microscopy, 3D single-particle tracking code, Code to compare single molecule data to ground truth coordinates, and Example raw SMLFM datasets. Single molecule light field microscopy reconstruction Authors: Ruth R. Sims, Kevin O'Holleran, Sohaib Abdul Rehman, Ezra Bruggeman and Sam Daly Objective: It takes in 2D localisation data (x,y) captured on a fourier light field microscope and turns it into 3D localisations (x,y,z). It does this by first assigning (x,y) to (x,y,u,v) space and using microscope parameters to calculate z position via parallax. Example data has been included (example_data_bcr_fixed_bcell.csv), which comprises 5,000 frames of a whole B cell membrane captured using single molecule light field microscopy. For more information, see: https://doi.org/10.1364/OPTICA.397172Test Single-particle tracking code Groups 3D coordinates from a .csv file (i.e. [x y z frame]) into molecular trajectories based on user defined metrics. This code incorporates track.m by John C. Crocker (University of Chicago) and MLEs by Joseph S. Beckwith (University of Cambridge). For further details see the description within the tracking functions. Example 3D data can be found in the folder 'example_data_bcr_tracking' that comprises some single particle tracking data collected from live B cells. The parameters contained in the distributed code enable instant 3D reconstruction of single trajectories of BCRs. Matching codes These scripts match fitted 2D/3D localisation datasets derived from simulations with their ground truth coodinates to determine positive predictive value and sensitivity for different 3D PSFs at increasing density. Example raw localization datasets have been included for the standard PSF. To begin, run Standard.m and select the directory containing subfolders 'numEmittersPerFrame_X'. Example Raw Data Example raw SMLFM datasets to ... |
| نوع الوثيقة: | software |
| اللغة: | English |
| العلاقة: | https://zenodo.org/record/8190164Test; https://doi.org/10.5281/zenodo.8190164Test; oai:zenodo.org:8190164 |
| DOI: | 10.5281/zenodo.8190164 |
| الإتاحة: | https://doi.org/10.5281/zenodo.8190164Test https://doi.org/10.1101/2023.05.02.539032Test https://doi.org/10.5281/zenodo.8190163Test https://zenodo.org/record/8190164Test |
| حقوق: | info:eu-repo/semantics/openAccess ; https://creativecommons.org/licenses/by/4.0/legalcodeTest |
| رقم الانضمام: | edsbas.D5E2F60E |
| قاعدة البيانات: | BASE |
| ResultId |
1 |
|---|---|
| Header |
edsbas BASE edsbas.D5E2F60E 897 3 Electronic Resource electronicResource 897.149658203125 |
| PLink |
https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&scope=site&db=edsbas&AN=edsbas.D5E2F60E&custid=s6537998&authtype=sso |
| FullText |
Array
(
[Availability] => 0
)
Array ( [0] => Array ( [Url] => https://doi.org/10.5281/zenodo.8190164# [Name] => EDS - BASE [Category] => fullText [Text] => View record in BASE [MouseOverText] => View record in BASE ) ) |
| Items |
Array
(
[Name] => Title
[Label] => Title
[Group] => Ti
[Data] => High-density volumetric super-resolution microscopy
)
Array ( [Name] => Author [Label] => Authors [Group] => Au [Data] => <searchLink fieldCode="AR" term="%22Daly%2C+Sam%22">Daly, Sam</searchLink><br /><searchLink fieldCode="AR" term="%22Ferreira+Fernandes%2C+João%22">Ferreira Fernandes, João</searchLink><br /><searchLink fieldCode="AR" term="%22Bruggeman%2C+Ezra%22">Bruggeman, Ezra</searchLink><br /><searchLink fieldCode="AR" term="%22Handa%2C+Anoushka%22">Handa, Anoushka</searchLink><br /><searchLink fieldCode="AR" term="%22Peters%2C+Ruby%22">Peters, Ruby</searchLink><br /><searchLink fieldCode="AR" term="%22Benaissa%2C+Sarah%22">Benaissa, Sarah</searchLink><br /><searchLink fieldCode="AR" term="%22Zhang%2C+Boya%22">Zhang, Boya</searchLink><br /><searchLink fieldCode="AR" term="%22Beckwith%2C+Joseph+S%2E%22">Beckwith, Joseph S.</searchLink><br /><searchLink fieldCode="AR" term="%22Sanders%2C+Edward+W%2E%22">Sanders, Edward W.</searchLink><br /><searchLink fieldCode="AR" term="%22Sims%2C+Ruth+R%2E%22">Sims, Ruth R.</searchLink><br /><searchLink fieldCode="AR" term="%22Klenerman%2C+David%22">Klenerman, David</searchLink><br /><searchLink fieldCode="AR" term="%22Davis%2C+Simon+J%2E%22">Davis, Simon J.</searchLink><br /><searchLink fieldCode="AR" term="%22O'Holleran%2C+Kevin%22">O'Holleran, Kevin</searchLink><br /><searchLink fieldCode="AR" term="%22Lee%2C+Steven+F%2E%22">Lee, Steven F.</searchLink> ) Array ( [Name] => DatePubCY [Label] => Publication Year [Group] => Date [Data] => 2023 ) Array ( [Name] => Subset [Label] => Collection [Group] => HoldingsInfo [Data] => Zenodo ) Array ( [Name] => Subject [Label] => Subject Terms [Group] => Su [Data] => <searchLink fieldCode="DE" term="%22super-resolution+microscopy%22">super-resolution microscopy</searchLink><br /><searchLink fieldCode="DE" term="%22single+molecule+light+field+microscopy%22">single molecule light field microscopy</searchLink><br /><searchLink fieldCode="DE" term="%22single+particle+tracking%22">single particle tracking</searchLink> ) Array ( [Name] => Abstract [Label] => Description [Group] => Ab [Data] => Overview Code and example data associated with 'High-density volumetric super-resolution microscopy' by Daly et al. including: 3D reconstruction code for single molecule light field microscopy, 3D single-particle tracking code, Code to compare single molecule data to ground truth coordinates, and Example raw SMLFM datasets. Single molecule light field microscopy reconstruction Authors: Ruth R. Sims, Kevin O'Holleran, Sohaib Abdul Rehman, Ezra Bruggeman and Sam Daly Objective: It takes in 2D localisation data (x,y) captured on a fourier light field microscope and turns it into 3D localisations (x,y,z). It does this by first assigning (x,y) to (x,y,u,v) space and using microscope parameters to calculate z position via parallax. Example data has been included (example_data_bcr_fixed_bcell.csv), which comprises 5,000 frames of a whole B cell membrane captured using single molecule light field microscopy. For more information, see: https://doi.org/10.1364/OPTICA.397172 Single-particle tracking code Groups 3D coordinates from a .csv file (i.e. [x y z frame]) into molecular trajectories based on user defined metrics. This code incorporates track.m by John C. Crocker (University of Chicago) and MLEs by Joseph S. Beckwith (University of Cambridge). For further details see the description within the tracking functions. Example 3D data can be found in the folder 'example_data_bcr_tracking' that comprises some single particle tracking data collected from live B cells. The parameters contained in the distributed code enable instant 3D reconstruction of single trajectories of BCRs. Matching codes These scripts match fitted 2D/3D localisation datasets derived from simulations with their ground truth coodinates to determine positive predictive value and sensitivity for different 3D PSFs at increasing density. Example raw localization datasets have been included for the standard PSF. To begin, run Standard.m and select the directory containing subfolders 'numEmittersPerFrame_X'. Example Raw Data Example raw SMLFM datasets to ... ) Array ( [Name] => TypeDocument [Label] => Document Type [Group] => TypDoc [Data] => software ) Array ( [Name] => Language [Label] => Language [Group] => Lang [Data] => English ) Array ( [Name] => NoteTitleSource [Label] => Relation [Group] => SrcInfo [Data] => https://zenodo.org/record/8190164; https://doi.org/10.5281/zenodo.8190164; oai:zenodo.org:8190164 ) Array ( [Name] => DOI [Label] => DOI [Group] => ID [Data] => 10.5281/zenodo.8190164 ) Array ( [Name] => URL [Label] => Availability [Group] => URL [Data] => https://doi.org/10.5281/zenodo.8190164<br />https://doi.org/10.1101/2023.05.02.539032<br />https://doi.org/10.5281/zenodo.8190163<br />https://zenodo.org/record/8190164 ) Array ( [Name] => Copyright [Label] => Rights [Group] => Cpyrght [Data] => info:eu-repo/semantics/openAccess ; https://creativecommons.org/licenses/by/4.0/legalcode ) Array ( [Name] => AN [Label] => Accession Number [Group] => ID [Data] => edsbas.D5E2F60E ) |
| RecordInfo |
Array
(
[BibEntity] => Array
(
[Identifiers] => Array
(
[0] => Array
(
[Type] => doi
[Value] => 10.5281/zenodo.8190164
)
)
[Languages] => Array
(
[0] => Array
(
[Text] => English
)
)
[Subjects] => Array
(
[0] => Array
(
[SubjectFull] => super-resolution microscopy
[Type] => general
)
[1] => Array
(
[SubjectFull] => single molecule light field microscopy
[Type] => general
)
[2] => Array
(
[SubjectFull] => single particle tracking
[Type] => general
)
)
[Titles] => Array
(
[0] => Array
(
[TitleFull] => High-density volumetric super-resolution microscopy
[Type] => main
)
)
)
[BibRelationships] => Array
(
[HasContributorRelationships] => Array
(
[0] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Daly, Sam
)
)
)
[1] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Ferreira Fernandes, João
)
)
)
[2] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Bruggeman, Ezra
)
)
)
[3] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Handa, Anoushka
)
)
)
[4] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Peters, Ruby
)
)
)
[5] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Benaissa, Sarah
)
)
)
[6] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Zhang, Boya
)
)
)
[7] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Beckwith, Joseph S.
)
)
)
[8] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Sanders, Edward W.
)
)
)
[9] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Sims, Ruth R.
)
)
)
[10] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Klenerman, David
)
)
)
[11] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Davis, Simon J.
)
)
)
[12] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => O'Holleran, Kevin
)
)
)
[13] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Lee, Steven F.
)
)
)
)
[IsPartOfRelationships] => Array
(
[0] => Array
(
[BibEntity] => Array
(
[Dates] => Array
(
[0] => Array
(
[D] => 01
[M] => 01
[Type] => published
[Y] => 2023
)
)
[Identifiers] => Array
(
[0] => Array
(
[Type] => issn-locals
[Value] => edsbas
)
[1] => Array
(
[Type] => issn-locals
[Value] => edsbas.oa
)
)
)
)
)
)
)
|
| IllustrationInfo |