Difference between revisions of "Pictures"

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[[File:PictureE1.png]]
 
[[File:PictureE1.png]]
  
 
NB: The size of the original TIFF file varies from 1 to 20 MB (in the examples observed till now). In order to minimize the space, the cropped images will be converted into JPEG files (50-100KB).Bigger images shown in the gene expression summary page will affect the speed of loading the page. We have the parental image for users access if they need high resolution. 
 
 
'''Question to web team: is PNG file format) a good choice? Are screenshots OK or the image should be always cropped in photoshop and saved as PNG file?'''-> Yes (Answer from TH october 6th). DR: we will create images of different sizes and see what fits best. TH suggests to try  3 images size :
 
- thumbnail -> 100  pixels width
 
- small -> 250 pixels width
 
- large -> 500 pixels width
 
 
Whenever we will ha pictures different from TIFF files (e.g. eps) we will rasterize them and convert into TIFF.
 
Supplementary material is generally stored by journals as PDF files. The PDF is converted in TIFF for consistency.
 
  
 
'''Special case:''' what do I do when one single panel refers to multiple genes. E.g. In the example below, panel B displays the expression of 3 different genes. We will simply name the pictures Fig3_B1, Fig3_B2, Fig3_B3.  
 
'''Special case:''' what do I do when one single panel refers to multiple genes. E.g. In the example below, panel B displays the expression of 3 different genes. We will simply name the pictures Fig3_B1, Fig3_B2, Fig3_B3.  
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===Picture size===
+
===Picture size and format===
 +
 
 +
All the pictures should be in JPEG format, if possible.
  
 
The picture size for thumbnails shown in the main gene expression page should be 200x200 pixels.
 
The picture size for thumbnails shown in the main gene expression page should be 200x200 pixels.

Revision as of 19:10, 18 October 2010

links to relevant pages
Caltech documentation
Pictures


Picture Curation

The immediate goal of picture curation is to be able to obtain images of gene expression data from the literature and individual laboratories and display them in the WormBase gene expression page.

  • We want display images related to the temporal or spatial (e.g., tissue, subcellular, etc.) localization of any gene in a wild-type background with different data types
    • Reporter gene analysis
    • Antibody staining
    • In situ hybridization
    • RT-PCR
    • Western or Northern blot data

Pipeline

In the early phases of curation, pictures will be taken from open access journals (e.g. PLoS). During the process of PLoS image curation, other publishers will be contacted for obtaining copyright permissions.

The images should be saved and stored according to the following guidelines. The example shown below refers to a PLoS Biology paper but the rules of handling the pictures are universal and not "paper specific".


Overview

This is a mock page of the expression page for gene K07C11.4. We would like to see highlighted panel B and F with the figure capture describing the expression of the gene AND be able to access the original figure by clicking the "See original figure" button.

PictureH.png

Downloading and saving the images

Pictures are downloaded in TIFF format from the original paper.

PictureA.png


Pictures are saved with their original name in order to minimize editing from the curator. In this case the file is called “journal.pbio.0020352.g006”.

The file is saved in a directory named after the WB paper ID. E.g.: WBPaper00024505, meaning that picture “journal.pbio.0020352.g006” has been downloaded from WBPaper00024505.


PictureB.png

These 2 numbers together WBPaper00024505_journal.pbio.0020352.g006 will be UNIQUE IDENTIFIERS of the object, that we call Picture object 1 (WBPicture000000001). The ID WBPicture000000001 will be the NAME of the object (?Picture) in the Picture Data Model.

The path WBPaper00024505_journal.pbio.0020352.g006 will define the SOURCE of the object in the Picture Data Model.

Now look at the picture above: In our WormBase expression pattern page we don’t want to display the whole picture because it contains information not pertinent to the expression data. We therefore need to CROP the 2 pictures depicting expression of the gene in the Wild Type. We want to have only panel B and F.

Each panel is cropped from the original picture in Photoshop and the files are saved as “journal.pbio.0020352.g006_B” “journal.pbio.0020352.g006_F” in the same directory as before: WBPaper00024505

PictureC.png


These will be respectively Picture object 2(WBPicture000000002) and Picture object 3 (WBPicture000000003).


To summarize till now:

Picture object 1: WBPicture000000001: WBPaper00024505_journal.pbio.0020352.g006

Picture object 2 WBPicture000000002: WBPaper00024505_journal.pbio.0020352.g006_B

Picture object 3: WBPicture000000003: WBPaper00024505_journal.pbio.0020352.g006_F

where WBPicture000000001 corresponds to the NAME of the object in the picture data model and WBPaper00024505_ journal.pbio.0020352.g006 corresponds to the SOURCE of the object in the Picture Data Model.

Question to web team: is it OK to keep the file names as proposed? -> Yes (Answer from TH october 6th)


At the same time, the text file associated with the entire figure WBPicture000000001, is saved with the same name as the figure -journal.pbio.0020352.g006- with a .doc extension. In this way we can make sure which figure legend goes with which picture. This .doc file is per se irrelevant for picture curation as the figure legend will be inserted in the "description" tag in the Picture Data Model.


PictureE1.png


Special case: what do I do when one single panel refers to multiple genes. E.g. In the example below, panel B displays the expression of 3 different genes. We will simply name the pictures Fig3_B1, Fig3_B2, Fig3_B3.


PictureG1.png

Let's go one step further...

Picture lineage

Picture object 1 is our PARENTAL IMAGE, we will display it only when the user will click on a “see original figure” link. Picture Objects 2 and 3 are our Daughter Images, which will be displayed on the gene expression page. See mock page below for a visual example:


PictureD1.png


We would like to keep the lineage relationship in order to know how images should be handled. In other words, we would like to know which image should be displayed in the expression pattern page and which should be displayed next to the "See original figure" link. For that purpose, in the Picture Data Model we have the "Image lineage" tag.


PictureK.png


There are cases in which parental image = daughter image. See picture below.


PictureL.png

Question to the web team: in this case is the Picture Data Model proposed sufficient to determine that this picture should be displayed as PARENTAL or DAUGHTER? Answer Yes


Picture size and format

All the pictures should be in JPEG format, if possible.

The picture size for thumbnails shown in the main gene expression page should be 200x200 pixels.

Picture size for the full view 600x600 pixels.

Picture size for the original file will be as big as needed.

NB: a note on 200x200 and 600x600 pixel size. This will not distort the pictures but just put a constraint on the maximum size of the thumbnail or the full image.

PictureM1.png

Picture Data Model Proposal

////////////////////////////////////////////////////////////////////////////////////

?Picture      Description ?Text
              Source ?Text
              Image_lineage Crop_picture ?Picture XREF Cropped_from
                            Cropped_from ?Picture XREF Crop_picture
              Pick_me_to_call Text Text
              Expr_pattern ?Expr_pattern XREF Picture
              Reference ?Paper XREF Picture
              Remark ?Text #Evidence
              GO_term      ?GO_term      XREF Pictures  
              Anatomy_term ?Anatomy_term XREF Picture 
///////////////////////////////////////////////////////////////////////////////////

Picture Data Model step by step explanation

Picture

Name of the picture object. E.g. WBPicture0000000001

Description

Figure legend

Source

For actual picture names. This is the name of the path leading to the picture file. The source includes the name of the directory where the picture comes from AND the name of the picture file. e.g. WBPaper00024505_journal.pbio.0020352.g006

Image Lineage

This is the picture object lineage. Large figures will be cropped into sections when they represent different data. We want to maintain the picture lineage -> by clicking on the "see original figure button" we want to access the entire image.

Pick_me_to_call

It is probably an XACE command to call the image. Asked via the Wormbase Dev mailing list. Waiting for answer

Expr_pattern

For linking to Expr-pattern data. This will be the Expr_pattern object that is associated with the picture

Reference

For the source of the picture E.g.WBPaper12345678

Remark

For curator notes this tag will be also used when the picture is coming from a lab and not from a publication. E.g. Picture provided by Ian Hope

GO_Term

This links to the GO term e.g. if a picture depicts sub-cellular localization

Anatomy_term

It will link the picture object directly to an Anatomy Object


Picture conversion

cd Desktop/WormBase/PLoS/Gene<tab>/ enterthis let me choose the directory from where I get the files

scp -r <directory_name I have chosen before> acedb@tazendra.caltech.edu:draciti/pictures/ enter I copy a folder and all its files into tazendra <enter password>

Open a new terminal

ssh acedb@tazendra.caltech.edu enter login into tazendra <enter password>

cd draciti/pictures/ enter this is the directory in tazendra where I will put my files cd <directory name> enter you can type ls for a list of files present in the directory igal2 -bigy 400 enter the program converts the pictures, bigy 400 is an arbitrary size for vertical pixels

ls -al it will list all the files present

If you want to open a new command window just press command+N on keyboard

the folder for getting the converted picures is called Incoming from Tazendra. We want to bring the files back: cd Desktop/Incoming\ from\ Tazendra/ enter

scp -r acedb@tazendra.caltech.edu:draciti/pictures/WBPaper00024399 . enter


(ssh = secure shell) (scp = secure copy

scp -r = recursive secure copy for directories)

(cd = change directory) pwd - show current directory