Tag: Count

DeadEasy Neurons – Count Neuronal Nuclei Stained with HB9 in whole Drosophila Embryos

DeadEasy Neurons

:: DESCRIPTION

DeadEasy Neurons is an imageJ plug-in allows you to count automatically neuronal nuclei stained with HB9 in whole Drosophila embryos. The plug-in was optimised to run with stacks of images with 0.245*0.245*0.245 cubic micron voxels.

::DEVELOPER

Alicia Hidalgo lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DeadEasy Neurons

:: MORE INFORMATION

Citation

Forero MG, Pennack JA, and Hidalgo A. (2010)
DeadEasy neurons: Automatic counting of HB9 neuronal nuclei in Drosophila. 
Cytometry, 77A: 371–378. doi: 10.1002/cyto.a.20877

BBSeq 1.0 – Analysis of RNA Sequence Count Data

BBSeq 1.0

:: DESCRIPTION

BBSeq  (Beta-Binomial modeling of the overdispersion of the RNA-seq count data)is used to identify differential expression in high-throughput count data, such as RNAseq count data which is derived from next-generation sequencing machines. Our modeling design is very flexible. It can not only solve the data with multiple comparisons, but also can find the affect from other covariates, such as age and other counfounding variables.

::DEVELOPER

Yi-Hui Zhou

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 BBSeq

:: MORE INFORMATION

Citation

Zhou YH, Xia K, Wright FA. (2011)
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Bioinformatics (2011) 27 (19): 2672-2678.

ParaCountStudio 3.1.0 – Count Cell Numbers within Image

ParaCountStudio 3.1.0

:: DESCRIPTION

ParaCountStudio is a program to count cell numbers within an image.ParaCountStudio has been developed to aid biologists needing to count large numbers of cells. It is a computer program written in Java that counts the number of cells that appear in an image, assuming a round cell shape and some degree of cell separation (ie. not tissues). The program has specifically been designed to distinguish red blood cells infected (or not) with malaria and stained with Giemsa, but the program is quite versatile and may work in a variety of other situations.

::DEVELOPER

Suzanne J Thomas. @ WEHI Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 ParaCountStudio

:: MORE INFORMATION

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