Van Oudenaarden Lab:ImProToo

Image Processing Tools - Repository for the AvO lab

Image Processing Tools - Repository for the AvO lab
You dont have to reinvent the wheel. This page contains a list of functions we commonly use in analyzing microscope data. The programs here are in a state of flux and may not even be working versions. However, the essential algorithm can be adapted to fit your needs. If you add to the capability of existing functions then please upload your versions so that all may profit by your cleverness! Please provide a 2-3 sentence description of your algorithm-describing the problem you are considering and outlining the methods you use.

Technical Keywords: Nuclei segmentation, Spot Counting, Worm Geometry, Z-Stack cleaning, Background correction Method Keywords: RNA FISH, GFP, Antibody, DNA FISH, Time-Lapse, Confocal, Epi, Trans

C. elegans L.x

 * [[Media:readmm.m|readmm.m]] Extremely quick stk reader by Arjun. Reads stk file 10X faster than tiffread2
 * [[Media:Tiffread2.m|tiffread2.m]] Reading Stack files
 * Background Corrections
 * Worm Straightening
 * Worm Stitching
 * Spot Counting
 * [[Media:LOG_filter.m|LOG_filter.m]] Run the raw image data through a linear filter designed to enhance particulate signals. [Arjun]
 * [[Media:count_mrna.m|count_mrna.m]] Count the number of spots in the image for all possible thresholds.[Arjun]
 * [[Media:multithreshstack.m|multithreshstack.m]] Manually identify the threshold by looking for a "plateau" region in graph of number of mRNAs as a function of the threshold.[Arjun]
 * Annotating Nucleii


 * Dong Hyun WNT analysis codes- Includes filtering, spot counting adaptive and manual, setting up local worm coordinates and stitching images. [[Media:DHwormcodes.zip|DHwormcodes.zip]]

C. elegans Jeroen's VPC analysis code

 * [[Media:analysis.zip|analysis.zip]] This contains the updated, streamlined version of the code below. It contains routines to annotate the worm(VPC), find mRNA fish spots and then display the data

Here is a summary: annotateWorm.m -	1) find points of interest (POI, in my case nuclei of VPCs)			2) find region of interest (ROI, in my case the area in the worm where the VPCs are) 3) find gonad axis

subroutines:		output:

getPOI.m		POI*.mat getVPC_ROI.m		VPC_ROI*.mat getGonadAxis.m		gonadAxis*.mat

findMRNA.m - 	find all mRNA spots and assign them to the correct VPC/Pn.p cell.

subroutines:		output: filterSpotData.m	filteredSpotData*.mat getThresholds.m		spotThresholds*.mat findSpots.m		spotCoordinates*.mat getMRNAperVPC.m		VPC_mRNA*.mat combineWormData.m -	Calculates a number of properties for the data set described in the input file: 1) Calculate mRNA vs gonad length (saved as  and )			2) Calculate average mRNA in each cell in all lineages binned for gonad length (saved as )

output: .mat

makeCombinedDataFigure.m -	Example of plotting 1) mRNA vs gonad length and 2) average mRNA in each cell in all lineages

subroutine: construct2DmRNAfig.m (for plotting mRNA in individual cells binnen for gonad length)

Example input file :

name   Lin-12 root   E:\Jeroen path   8-5-2009\lin-12_A592_lag-2_Cy5_26-40hrs_batch1 channel 1 Lbins  200 100 1500 Pnp    20 600 700 8000 Pnpx   80 900 1000 11000 Pnpxx  110 1200 1300 14000
 * [[Media:findAxisIntersection.m|findAxisIntersection.m]] blabla
 * [[Media:vulva.zip|vulva.zip]] This contains all the m files I use for FISH analysis (and quite a bit more files that are obsolete). It is quite a mess but look at the files with the more recent date for the most up to date version of what I do.
 * [[Media:timelapse.zip|timelapse.zip]] This contains all the file for timelapse experiments: finding axes, straightening and making movies

C. elegans Embryos

 * for instance, this
 * or this
 * or even this

Yeast
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Mammalian Cells
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Cyano-Bacteria
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Upload documents
you can upload a file from the "Upload file" link to the left

you can link that file to your page with something like this :

[[Media:Test.doc]]

you can do the same thing and name it something fancy like this :

[[Media:Test.doc|something fancy]]