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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @haesleinhuepf: Upgrading #ImageJ #autocomplete: Suggestions for user defined functions and variables - because people asked for it. Fr…
About 16 hours, 10 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @biorxivpreprint: Myosoft: an automated muscle histology analysis tool using machine learning algorithm utilizing FIJI/ImageJ software.…
About 16 hours, 10 mins ago by: Kota Miura (@cmci_)

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RT @ltuckerkellogg: Several great Computation Biology postdoc jobs have been posted at https://t.co/ahPafWjyVP in machine learning, dynamic…
About 2 days, 21 hours ago by: Kota Miura (@cmci_)

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RT @JCellBiol: Cross-linker–mediated regulation of #actin network organization controls tissue #morphogenesis, say Krueger et al @embl http…
About 4 days, 22 hours ago by: Kota Miura (@cmci_)

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RT @Dev_journal: "QuBiT: a quantitative tool for analyzing epithelial tubes reveals unexpected patterns of organization in the Drosophila t…
About 4 days, 23 hours ago by: Kota Miura (@cmci_)

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RT @ijmacros: Check out our paper in the Journal of Neuroscience Methods - 'A Versatile Macro-Based Neurohistological Image Analysis Suite…
About 4 days, 23 hours ago by: Kota Miura (@cmci_)
mainpages:linksvideo

Video Links

ImageJ Tutorials

ImageJ installation in Windows (2 min 30 sec)

Tutorial 01 Installing and Basics of ImageJ (46 min)

ImageJ tutorial (71 min)

Optimizing epifluorescence images (7min 40sec)

Particle Counting (7 min)

  1. Showing how to use [Analyze > Analyze Prticles…]

js9ECPuoOwA?.swf

Cell Area Measurement

- Segment cells using automatic thresholding, select cells using “magic wand” tool, store ROIs in roi manager.

WxTu2fn7QxY?.swf

Measure Intensity Changes over Time

  1. This tutorial uses MBF package so the menu structure is different from the bare ImageJ. You could do the same with legacy ImageJ by [Image > Stacks > Plot Z-axis Profile].

Gv7sJ7L2rRY?.swf

Automatic Nucleus Counting (ITCN Plugin)

Track and analyze Brownian Motions (MTrack2 plugin)

  1. Uses plugin “MTrack2” by Nico, and Excel to analyze tracks.

MDIVDAIkdME?.swf

Visualizing 3D (3Dviewer plugin)

Videos showing how to use 3D viewer, a plugin written by Benjamin Schmid. If you install Fiji, this plugin comes along with the installation.

  1. part 1

cD3Hc3NYkaU?.swf

  1. part 2

GqG_RcK3kYg?.swf

mainpages/linksvideo.txt · Last modified: 2016/05/24 05:46 (external edit)