Van Oudenaarden Lab:ImProToo: Difference between revisions
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==== C. elegans L.x==== | ==== 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 | * [[Media:Tiffread2.m|tiffread2.m]] Reading Stack files | ||
*Background Corrections | *Background Corrections | ||
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** [[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] | ** [[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 | *Annotating Nucleii | ||
==== C. elegans Jeroen's VPC analysis code==== | ==== C. elegans Jeroen's VPC analysis code==== | ||
* [[Media:findAxisIntersection.m|findAxisIntersection.m]] blabla | * [[Media:findAxisIntersection.m|findAxisIntersection.m]] blabla | ||
Revision as of 19:08, 3 July 2009
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: FISH (by Def. RNA), GFP, Antibody, DNA FISH, Time-Lapse, Confocal, Epi, Trans
C elegans
C. elegans L.x
- readmm.m Extremely quick stk reader by Arjun. Reads stk file 10X faster than tiffread2
- tiffread2.m Reading Stack files
- Background Corrections
- Worm Straightening
- Worm Stitching
- Spot Counting
- LOG_filter.m Run the raw image data through a linear filter designed to enhance particulate signals. [Arjun]
- count_mrna.m Count the number of spots in the image for all possible thresholds.[Arjun]
- 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
C. elegans Jeroen's VPC analysis code
- findAxisIntersection.m blabla
- 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.
- 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
you can add text like this.you can add text like this.
Mammalian Cells
you can add text like this.you can add text like this.
Cyano-Bacteria
you can add text like this.you can add text like this.
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 :
you can do the same thing and name it something fancy like this :
