Scmd saccharomyces cerevisiae morphological database
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SCMD: Saccharomyces Cerevisiae Morphological Database. Taro L. Saito 1,2 , Miwaka Ohtani 1,2 , Hiroshi Sawai 2 , Fumi Sano 2,4 , Ayaka Saka 2,4 , Daisuke Watanabe 2,4 , Masashi Yukawa 2,4 , Yoshikazu Ohya 2,4 and Shinichi Morishita *,2,3.

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SCMD: Saccharomyces Cerevisiae Morphological Database

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Scmd saccharomyces cerevisiae morphological database

SCMD:Saccharomyces Cerevisiae Morphological Database

Taro L. Saito1,2, Miwaka Ohtani1,2,

Hiroshi Sawai2, Fumi Sano2,4,

Ayaka Saka2,4, Daisuke Watanabe2,4, Masashi Yukawa2,4,

Yoshikazu Ohya2,4 and Shinichi Morishita*,2,3

  • Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo

  • 2.Institute for Bioinformatics and Research and Development, Japan Science and Technology Corporation

  • 3. Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo

  • 4.Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo


What is scmd

What is SCMD ?

  • SCMD is a collection of micrographs of budding yeast mutants.

  • Our image processing program, called CalMorph, clips individual cells from micrographs, then analyzes the characteristics of them.

  • Currently following number of yeast mutants and their micrographs are analyzed.

    • Mutants analyzed: 4,495

    • Micrographs Processed: 84,407 (x 3)

    • Cells retrieved:1,643,835


Micrographs

Micrographs

  • Three type of stains are used to see

    • Cell wall

      • FITC-ConA

    • Nucleus location

      • DAPI

    • Actin distribution

      • Rh-ph

  • All micrographs can be seen in the viewer provided in SCMD

Cell wall

Nucleus

Actin

image processing


Scmd saccharomyces cerevisiae morphological database

stain

FITC-ConA

DAPI

Rh-ph


Cell parameters

Cell Parameters


Categorizing by bud size

Categorizing by Bud Size

  • View of ‘group by bud size’

no bud

small

medium

large

yor202w his3


Nucleus location categories

Nucleus Location Categories

  • We categorized the states of nucleus locations into 7 groups.

  • State A, A1, B, C are regular status.

  • State D, E, F seldom occur.


Categorizing by nucleus location

Categorizing by Nucleus Location

  • View of ‘group by nucleus location’

A

A1

B

C

ybl052c sas3


Actin localization categories

Actin Localization Categories


Categorizing by actin localization

Categorizing by Actin Localization

  • View of ‘group by actin localization’

A

B

iso

api

E

F


Morphology search interface

Morphology Search Interface


Searching similar shape mutants

Searching Similar Shape Mutants

input shape

query result


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