starrynite II 20150713 – Accurate, Probabilistic Tracking for Single Cell analysis and understanding

starrynite II 20150713

:: DESCRIPTION

starrynite is an image analysis tool for tracking fluorescently-labeled nuclei during C. elegans embryogenesis.

::DEVELOPER

starrynite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 starrynite

:: MORE INFORMATION

Citation:

A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D,
Santella A, Du Z, Nowotschin S, Hadjantonakis AK and Bao Z
BMC Bioinformatics 2010, 11:580

nextflu 1.0 – Real-time Tracking of Influenza Evolution

nextflu 1.0

:: DESCRIPTION

nextflu is designed to perform near real-time tracking of influenza virus evolution.

::DEVELOPER

bedford lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web server

:: DOWNLOAD

 nextflu

:: MORE INFORMATION

Citation:

nextflu: real-time tracking of seasonal influenza virus evolution in humans.
Neher RA, Bedford T.
Bioinformatics. 2015 Jun 26. pii: btv381.

LEVER – Stem Cell Segmentation, Tracking and Lineaging

LEVER

:: DESCRIPTION

LEVER (Lineage Editing and Validation) is a collection of software tools for analyzing the development of proliferating (dividing) cells in time-lapse microscopy image sequences. LEVER includes algorithms for segmentation, tracking and lineaging. LEVER also includes a user interface that allows the segmentation, tracking and lineaging results to be validated, with any errors in the automated processing easily identified and quickly corrected

CloneView is an incredibly useful tool for visualizing the results from the LEVER program together with the image data.

::DEVELOPER

computational image sequence analysis

:: SCREENSHOTS

LEVER

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 LEVER

:: MORE INFORMATION

Citation

LEVER: software tools for segmentation, tracking and lineaging of proliferating cells.
Winter M, Mankowski W, Wait E, Temple S, Cohen AR.
Bioinformatics. 2016 Jul 16. pii: btw406.

OpenFreezer 201402 – Laboratory Reagent Tracking and Workflow Management System

OpenFreezer 201402

:: DESCRIPTION

OpenFreezer is an open-source information management system for biological laboratories.The system tracks information on all reagents within the laboratory, including specific properties of each reagent (i.e. sequences, external identifiers), and on all the physical preparations of these reagents (storage locations, physical characteristics).

::DEVELOPER

OpenFreezer Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Apache
  • PHP
  • MySQL
  • BioPython
  • Python
  • ReportLab
  • Overlib

:: DOWNLOAD

   OpenFreezer

:: MORE INFORMATION

Citation

Nat Methods. 2011 Jul 28;8(8):612-3. doi: 10.1038/nmeth.1658.
OpenFreezer: a reagent information management software system.
Olhovsky M, Williton K, Dai AY, Pasculescu A, Lee JP, Goudreault M, Wells CD, Park JG, Gingras AC, Linding R, Pawson T, Colwill K.

CRISPRtrack 1.0.1 – Using CRISPR Spacer Content for Bacterial Species Tracking

CRISPRtrack 1.0.1

:: DESCRIPTION

CRISPRtrack uses CRISPR spacers as molecular markers to track bacterial strains.It can be used to estimate the microbiome similarity based on the sharing of CRISPR spacer contents between the microbiomes. It can also be used to quantify the retention of donor strains in recipients that receive microbiota transfer treatment (such as fecal microbiota transfer, FMT) using microbiome data.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE

:: DOWNLOAD

CRISPRtrack

:: MORE INFORMATION

Citation:

CRISPR J. 2019 Feb 1;2(1):41-50. doi: 10.1089/crispr.2018.0046. Epub 2019 Feb 14.
CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis.
Lam TJ, Ye Y.