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

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

slide4
stain

FITC-ConA

DAPI

Rh-ph

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

categorizing by actin localization
Categorizing by Actin Localization
  • View of ‘group by actin localization’

A

B

iso

api

E

F

searching similar shape mutants
Searching Similar Shape Mutants

input shape

query result

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