Whatfs SPI?

SPI (SuPerImposing system) is a tool for incorporating gene expression data into a four-dimensional database of C.elegans embryogenesis.

 

How to use SPI:

As shown in the figure below, SPI receives sequential images of fluorescent confocal microscopic data as input. Then, you select parameters for superimposition, such as cell stage. Finally, it superimposes input data onto the computer graphics framework. Furthermore, it reports the possibility for the input protein to be localized during C.elegans embryogenesis.

 

1.       Input image data

 

yInput image dataz

Acquisition of serial sections of fluorescent confocal images is shown with triple colors, that is, DAPI for nuclei, Cy-3 for the internal marker, which is a germline specific protein POS-1(#), and Cy-5 for one of the 56 maternal gene products.

(Please select a protocol from the top page of this Web site to see a detailed experiment method.)

 

Please satisfy confocal images which fulfill the following conditions.

<Essential conditions>

1.      Acquire confocal images of 40 upper and lower slices of one embryo.

2.      Image resolution is 256 x 256.

3.      Fix left-hand side to the anterior side.

4.      The embryo stage should be from the 2-cell stage to the 28-cell stage.

 

Please compress data which satisfy conditions in .tar form or .tar+gz form, and transmit.

(#)Tabara,H. et al.(1999) Development, 126, 1-11.

 

 

2.       Selection of some images to determine a threshold

 

yColor selectionz

Select the desired color item to create 3-dimensional computer graphics (3D-CG). (default color: Green)

 

yImage selectionz

Select the representation image used to determine the threshold of conversion as the 3D-CG by the VRML format.

Advice: At this time, only the slice picture of an odd number is displayed. Probably, the best-focused image will be best.

 

 

3. Setting of threshold and each parameter

 

yItem selectionz

Select the item created in 3D-CG. Two or more selections are possible.

 

ySetting of thresholdz

Input two kinds of thresholds to your QUERY to express strength of signal (default values: 50 and 100). Input a single threshold for POS-1 and DAPI. (default values: 50 and 100, respectively).

 

ySetting of Z-axis scalez

 Set the ratio of scales of Z-axis with respect to XY. (default value: 2)

 

y(Option) Setting of cell stagez

Input the value when you have already understood the cell stage. It is possible to superimpose it by specifying it with high-speed and accuracy.

When no input value is specified, our service predicts the cell stage.

 

yE-mail registrationz

Final calculation results and the file storage location are transmitted to the E-mail address that you registered. Registration of E-mail address is indispensable.

 

4. Display of input completion

After all input is registered, information and calculation ID of the input completion are displayed. Moreover, after all processing of our service ends, the output result is compressed and preserved in the Web server.

 

5. Output

 

The output result is saved on the Web server for 24 hours; the address will be sent to you by E-mail.

The output result is displayed from the left in order of the slice image in Quicktime form; 3D-CG is given in VRML form and the 3D is superimposed CG.

 

Download address:

(*) QuickTime player: http://www.apple.com/quicktime/download/support/index.html

(**) Cosmo player http://www.cai.com/cosmo/home.htm