image analysis in a plant cell context
416 views | +0 today
Follow
image analysis in a plant cell context
tools and strategies to analyze microscope images
Curated by Schattat Lab
Your new post is loading...
Your new post is loading...
Scooped by Schattat Lab
Scoop.it!

Time Gating of Chloroplast Autofluorescence Allows Clearer Fluorescence Imaging In Planta

Time Gating of Chloroplast Autofluorescence Allows Clearer Fluorescence Imaging  In Planta | image analysis in a plant cell context | Scoop.it
Chloroplast, an organelle facilitating photosynthesis, exhibits strong autofluorescence, which is an undesired background signal that restricts imaging experiments with exogenous fluorophore in plants. In this study, the autofluorescence was characterized in planta under confocal laser microscopy, and it was found that the time-gated imaging technique completely eliminates the autofluorescence. As a demonstration of the technique, a clearer signal of fluorescent protein-tagged phototropin, a blue-light photoreceptor localized at the chloroplast periphery, was visualized in planta .
Schattat Lab's insight:
Sounds interesting, I will have to look at it!
more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Youtube Videos from Annual Reviews

Schattat Lab's insight:
Always wanted to just lean back and to enjoy science in a non written form? With the Youtube Channel of Annual Reviews this is possible. I just came accross it and found it woth sharing. There are even interesting lectures about plant toppics. http://www.youtube.com/user/annualreviews/videos
more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Plant Image Analysis - Software

Plant Image Analysis - Software | image analysis in a plant cell context | Scoop.it

Website presenting the available plant image analysis softwares. This page is an amazing collection of hand pickend image Analysis tools for plant research!

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

CellPie Introduction

CellPie Introduction | image analysis in a plant cell context | Scoop.it

CellPie is a software to help analyze and evaluate the spatial pattern of cell distribution. A pie structure is designed to visulize the distribution along each direction and for certian stepsize. The interval of directions and size of step can be customized. It also includes the cell segmentation with color channel threshold.

 

Publication

Yang Tang, Min Tang, Alexander Annala, Rex A. Moats, CellPie: A Spatial Pattern Assessment Tool for Cellular Images. INFORMATION-An International Interdisciplinary Journal ,ISSN: 1343-4500, to appear.

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Analysis of Arabidopsis thaliana root growth kinetics with high temporal and spatial resolution

Analysis of Arabidopsis thaliana root growth kinetics with high temporal and spatial resolution | image analysis in a plant cell context | Scoop.it

Nima Yazdanbakhsh* and Joachim Fisahn

 

Ann Bot. 2010 May; 105(5): 783–791.

 

The high temporal resolution allows small modifications of total root elongation growth to be revealed. Furthermore, with the options to investigate growth of various mutants in diverse growth conditions the present tool allows modulations in root growth kinetics due to different biotic and abiotic stimuli to be unravelled. Measurements performed on Arabidopsis thaliana wild-type (Col0) plants revealed rhythms superimposed on root elongation. Results obtained from the starchless mutant pgm, however, present a clearly modified pattern. As expected, deviation is strongest during the dark period.

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Quantitative comparison of spot detection methods in live-cell fluorescence microscopy imaging

Quantitative comparison of spot detection methods in live-cell fluorescence microscopy imaging | image analysis in a plant cell context | Scoop.it

I just found this nice article about spot detection methods. Although it gets pretty mathematical but still is a nice review of approaches to spot detection.

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Actin-dependent plastid movement is required for motive force generation in directional nuclear movement in plant

Schattat Lab's insight:

This is a nice read about how cells rearrange according to changing light conditions. Plastids pull the nucleus into the shadow! How nice of them :)

 

more...
Schattat Lab's curator insight, March 31, 4:19 AM

This is a nice read about how cells rearrange according to changing light conditions. Plastids pull the nucleus into the shadow! How nice of them :)

 

Scooped by Schattat Lab
Scoop.it!

Taking Courses — iBiology

Taking Courses — iBiology | image analysis in a plant cell context | Scoop.it
Free iBiology video courses: Microscopy Short course, Microscopy Long course, Cell Biology Flipped Course.
Schattat Lab's insight:

Find nice videos, which teach you basics about microscopy. These machienes are not that complicated :)

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

SlideBook™ 5

SlideBook™ 5 | image analysis in a plant cell context | Scoop.it
SlideBook 5 is a comprehensive digital microscopy imaging package that carries biomedical research through experimental setup, data acquisition and image analysis.

 

A commercial tool I never heard of. Does anyone has experience with it?

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Icy

Icy | image analysis in a plant cell context | Scoop.it

See and test a fairly new imaging procesing software. It is free and it has a nice intuitive user interface!

 

"Icy: The open source community software for bio-imaging Over the past decades the image analysis community has put substantial efforts into developing algorithms for various applications, yet their visibility often remained clustered to a handful of people,

due to lack of proper means of communication and advertising. Meanwhile, numerous experts in the biology community have been turning to image analysis to answer their questions, and yet often fail to find adapted (or affordable) tools to fit their needs.
Icy provides an integrated platform that aims at bridging the gap between developers and users, by combining: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. "

more...
No comment yet.
Scooped by Schattat Lab
Scoop.it!

Spot detector based on a 3D LoG filter

Spot detector based on a 3D LoG filter | image analysis in a plant cell context | Scoop.it

Spot detector based on a 3D LoG filter

 

This PlugIn for ImageJ is pretty amazing in helping to enhance the visibility in noisy images. I tryed it with endosome images obtained with an standard LSM and it works well. In combination with the biary function spot detection works nice.

more...
No comment yet.