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Schnitzcells specifications


Unique identifier OMICS_05653
Name Schnitzcells
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained No


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Publication for Schnitzcells

Schnitzcells citations


Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations

PMCID: 5888573
PMID: 29432616
DOI: 10.1093/nar/gky079

[…]  15 nm) with an intensity of 320 mw and an exposure time of 250 ms. the emission filter was from chroma (texasred hyq lp 596, bp641/75)., microscopy images were analyzed with the matlab-based package schnitzcells (). we analyzed single-cell growth rate, mcherry fluorescence, cell length and cell cycle duration of a bottom cell in each microfluidic channel. single-cell growth was measured as the ce […]


Trajectory energy minimization for cell growth tracking and genealogy analysis

PMCID: 5451832
PMID: 28573031
DOI: 10.1098/rsos.170207

[…] inaccurate segmentation and tracking results []. third, to address the problems mentioned above, time-lapse images can be automatically processed and followed by manual editing and correcting. schnitzcells [] and microbetracker [] are two popular systems that can do quantitative analysis of fluorescent time-lapse images of living cells. however, such systems are laborious […]


Image analysis driven single cell analytics for systems microbiology

PMCID: 5379763
PMID: 28376782
DOI: 10.1186/s12918-017-0399-z

[…] vision []. for bacterial image processing, well known open source software packages for analyzing cell movies are the tlm-tracker [], celltracer [], microbetracker [] and its successor oufti [], and schnitzcells []. the tlm-tracker [] uses multiple alternative algorithms for cell segmentation, such as threshold-based, watershed transform and level-set methods. to construct the lineage tree […]


MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations

PMCID: 5610899
PMID: 28948108
DOI: 10.7717/peerj.3830

[…] time of 130 ms for phase contrast images; and exposure time of 200 ms (filter texasred u-mwg, ex. 510–550 nm, em. lp 590 nm) for mcherry images. cells were analyzed with the matlab-based package schnitzcells (), and segmented using mcherry fluorescence images., statistics was done in spss, r and microsoft excel. error bars in all graphs depict standard deviation from n replicates […]


In vivo single RNA tracking shows that most tRNA diffuses freely in live bacteria

PMCID: 5314786
PMID: 27625389
DOI: 10.1093/nar/gkw787

[…] of entire field-of-views containing 30–50 cells under continuous wave illumination in the respective fluorescence channel. cells were segmented automatically by adapting the matlab implementation ‘schnitzcells’ () for brightfield cell images. the manually adjusted cell masks were used to extract cells’ fluorescence data by calculating the total fluorescence intensity per cell area within […]


Fitness Trade Offs in Competence Differentiation of Bacillus subtilis

PMCID: 4896167
PMID: 27375604
DOI: 10.3389/fmicb.2016.00888

[…] contour. a threshold was then applied to the correlation images using a script developed in conjunction with anthony et al. (). after applying the threshold, images were imported into schnitzcells (young et al., ) for tracking, and lineages were analyzed using an in-house matlab script. in short, genealogy trees were drawn for each image set and generation time for every dividing […]

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Schnitzcells institution(s)
Division of Biology, California Institute of Technology, Pasadena, USA

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