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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @lauranetzzz: Sensible analysis of image datasets through ImageJ By Doreen A. Rios Min. participants 5 Max. participants 20 Duration…
About 6 hours, 29 mins ago by: Kota Miura (@cmci_)

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RT @achamess: Review of image analysis methods for spatial transcriptomics/proteomics? https://t.co/pfZBz9Z5jY
About 1 day ago by: Kota Miura (@cmci_)

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RT @J_N_Slayer: Have a cool method to study axon-specific molecular events, e.g. transport, translation? Consider submitting to our @JoVEJo
About 2 days, 4 hours ago by: Kota Miura (@cmci_)

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RT @jytinevez: I had a fantastic time teaching in beautiful Gothenburg for the CCI image analysis course. I slept for 12 hours after that…
About 2 days, 6 hours ago by: Kota Miura (@cmci_)

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RT @martinjones78: The advert for our next sandwich student placement (on shape quantification for volume EM) @EM_STP @TheCrick is now up!…
About 2 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @clathrin: It’s real! I just received an advance copy of my book “The Digital Cell”. Official release is 1st Dec. https://t.co/DaWIPAoeMY
About 2 days, 16 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)