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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation https://t.co/jECl7deOVG
About 9 hours, 11 mins ago by: Kota Miura (@cmci_)

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Impressive and swift moderation @helenajambor !
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz https://t.co/zOaMWvzd8k https://t.co/AXYBCeGyw6
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots https://t.co/QZE7xQtaa3
About 2 days, 19 hours ago by: Kota Miura (@cmci_)

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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 2 days, 23 hours ago by: Kota Miura (@cmci_)
shared:bias2013:assignments

Assignments

module 1 and 2

1. Quantum dot counting (planned, but omitted)

sample image: quantumdots.tif

design a protocol for segmenting quantum dot and write a macro that counts the number of quantum dots in the image.

2. Modify dot movement macro as you like.

(Brownian, Cycloid, Sinusoidal …)

Save your macro in the data server. Please do not forget to include your names in the macro file name.

Answers

module 4

Relative Movement

Go to section 4.4.7 and do the exercise 4.4.7-1.

PIV based anaysis (omitted)

Try install and using the following plugin: https://sites.google.com/site/qingzongtseng/piv

Get a vector field data (you need only two frames for this), save the results as a csv file and then analyze the directioanlity in R.

shared/bias2013/assignments.txt · Last modified: 2017/06/06 20:12 by kota