My major has NEVER be computer science ...
I finished my undergraduate in biochemistry, and have a graduate training in cell biology, none of which is related to coding. The following section includes files I have used for various purposes. They are usable, but ugly and buggy. If you have questions about the image analysis I did in my papers, please feel free to send me an email.
Matlab code
ImageJ macro
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Edge Ratio 
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Edge Ratio is a update of "Edge Measurement 2 macro". It will not only measure the raw values, but also give the percentage values and ratios between channels. This zip file has all the examples and a step-by-step manual. I also created a blog page for this code.
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Edge Measurement 2
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It is a update of the original version, which can handle any RGB tif file.
You can also use this version,
which will not process the region outside of the mask.
Process steps:
1. run this macro from ImageJ after you open a RGB tif file;
2. hand draw the region of interest, which will be analyzed by contour pixel extraction, and "Edit -> Selection -> Create Mask";
3. adjust the threshold, outline the whole target by using "Wand Tool", and "Edit -> Selection -> Create Mask"
4. the output is the excel file in the same directory, in which R/G/B channel is numbered in 0/1/2.
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RGB 2 montage
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This macro batch processes a folder of images including the sub-directory.
All the images must be in RGB TIFF format.
This macro will generate individual channel-view of the RGB file,
and make montage of both the original and the channel-view of the image.
The outputs start with M#-, which will be treated differently with original files,
and will be over-written when you re-run the macro.
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Channel Extend for Focus
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This macro batch processes a folder of images including the sub-directory.
All the images must be in stack TIFF format, which means having z-stack on each channel.
This macro utilizes Extended Depth of Focus ImageJ plugin to combine z-stack images,
which need you to click the Fusion button when needed.
Process steps:
1. stack de-interleaves according to the channel number;
2. use Extended Depth of Focus plugin generate fusion-view of each channel;
3. merge the first channel to red, second to green, third to blue of one RGB file.
This macro will generate the RGB merge file.
The outputs start with M#-, which will be treated differently with original files,
and will be over-written when you re-run the macro.
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Edge Measurement
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I created for barbed end assay, use RGB tif file
I Illustrated by "Expand/Shrink Selection" Michael Schmid, version 05-Nov-2004
Process steps:
1. run this macro from ImageJ after you select a RGB tif file;
2. the program will wait until a file named Mask is created.
I usually just convert the copied RGB tif to 8-bit, adjust the threshold,
use "Wand Tool" to have the right cell outline, and "Edit -> Selection -> Create Mask"
3. the information in the blot can be export to other programs for better quality.
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Perl script
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2shrna.pl
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1. Use Dharmacon siDESIGN Center to find functional siRNA sequences;
2. Input the siRNA sequence here to get the stem-loop oligos;
3. Order desalted oligos from Integrated DNA Technologies or other companies;
4. Do "wet" experiments.
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peptidemap21.pl
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Use for tryptic peptide map prediction.
1. install perl, python;
2. install matplotlib;
3. get the amino acid sequence for analysis;
4. label the possible phosphorylation sites with “-" after;
5. run the script peptidemap to get the PNG file.
* You can change the value of $clean or $phosp to get different outputs.
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01genome.pl
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Convert the DNA sequence in FAA format into binary system. [A->01, C->11, G->00, and T->10]
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count_ACGT.pl
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Count the number and percent of A/T/G/C in a DNA sequence.
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extract.pl
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Extract information from a Microsoft Access Database file and reform them into a XML file.
Based on wong's code.
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extract_dna.pl
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Extract DNA sequence and exclude the annotations.
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Find_ORFs.pl
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Identify all possible open reading frames from genome DNA sequence in FAA format.
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for_cterm_2.pl
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Modify the HTML files generated by the program Cterm2000.
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gbk2fna.pl
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Convert the GBK format file into FNA format. It is useful in evolution analysis based target.gbk files from NCBI.
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gbk2faa.pl
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Convert the GBK format file into FAA format. It is useful in evolution analysis based target.gbk files from NCBI.
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pic_lib.pl
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Construct web-pages for organizing a great number of pictures. Put this PERL file in the dir where big pictures are to generate the HTML files.
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PreProcess.pl
FindConserved.pl
GenOutputs.pl
IsConservedProtein.pl
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Analysis the genome of procaryote. Kindly provided by Ravi and Richard.
Step 1: Download BLAST to your local PC. Install BLAST.
Step 2: Download the bacteria species' .fna, .faa, and .gbk files to a data directory. Rename the files to [BacteriaName].fna, [BacteriaName].faa, and [BacteriaName].gbk.
Step 3: Copy PERL files to the data directory. They are PreProcess.pl, FindConserved.pl, IsConservedProtein.pl and GenOutputs.pl.
Step 4: Run PreProcess.pl in the data directory to pre-process the data files.
Step 5: Run FindConserved.pl in the data directory to search for the conserved proteins. The output of this program goes into score.out file. You can customize the search by modifying FindConserved.pl program. The variables are $threshold, $sampleName, and @targetNames.
Step 6: Check the score.out file. If the results look reasonable, then run GenOutputs.pl to generate the output files.
Step 7: Use the output files to run PHYLIP to generate a taxonomy tree. And IsConservedProtein.pl can be used to make confirmation.
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