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EMBL BioImage Data Analysis

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Timeline of @cmci_

cmci_ avatar

RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist https://t.co/I5
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 6 days, 1 hour ago by: Kota Miura (@cmci_)

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RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

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RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 1 day 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)