Scientific Volume Imaging b.v.

Scientific Volume Imaging b.v.
Laapersveld 63
1213 VB Hilversum, The Netherlands
http://www.svi.nl
http://support.svi.nl/wiki

This is part of the Sidb Tutorial. Previous: Sidb User Management

Upload

This section will help you to archive new images into the Webdriven 3D Image Database. Before you can upload your file, you have to fill in a few image data beside the location of the image you want to upload. This will make it a lot more easier to find your image back. Also you have to know the type of your file and you have to decide if you want to use a template. You can decide to make your image public for the whole group. Everybody can see the image and download it. The private image will only be shown to you. By doing the exercises you will get more used to upload an image. Starting with Upload

After you have clicked on the Upload button the upload screen will appear, here you will see some options. These options are respectively:

• The filetype of the image you want to upload
• The template you want to use

The image you want to upload has got a filetype. For example the file "faba64.ics" of the image "faba64" has got the type "ICS". To upload your image you have to select a template with information about the used microscope. You can select an existing template or select new template to create a new one.

In case you selected new template a form will appear.

• 'Templatename': the name of the template. You can fill in whatever you want.
• 'Position of the origin': fill in the position of the origin of the image.
• 'Samplingdistance': fill in the samplingdistance.
• 'Type sensor': fill in the type of the sensor. This has to be either text or numbers or other signs.
• 'Number of channels': fill in the number of channels that has been used.
• 'Dimensions of the sensor': fill in the dimensions of the sensor for each channel.
• 'Wavelength of the excitation': fill in wavelength of the excitation for each channel.
• 'Wavelength of the emission': fill in wavelength of the emission for each channel.
• 'Number of photons needed to excitate one colourmolecule': fill in number of photons needed to excitate one colourmolecule.
• 'Refractionindex of the medium': fill in refractionindex of the medium.
• 'Numerical aperture of the lense': fill in numerical aperture of the lense.
• 'Refractionindex of the medium for which the lens is designed': fill in refractionindex of the medium for which the lens is designed.

All fields except 'Templatename' and 'Type sensor' have to be numbers.

It is not mandatory to fill in everything whenever you create a new template. Only the name of the template has to be filled in. Each template has its own individual name, so there are no templates with the same name. Choose a name you haven't used before!

After typing your input data and confirming it by clicking add you will see the next page to upload. In case you selected an existing template you will see this page immediately after clicking the button add. Here you can select your image and its characteristics. Such as:

• 'Location of the image': you can fill in the directory of the file you want to upload or click on Browse to find it on your computer. If you want to upload an ISC file you have to select two locations: one for the ICS filen and another for the IDS file. Most of the time you can find these two files in the same directory.
• 'Ids-location' of the image: You can do this by clicking the button Browse.
• 'Description': A short description of this image.
• 'Private': If nobody but you is allowed to view this picture then select this checkbox. If you don't select it everybody is allowed to view the image.

It is not mandatory to fill in everything whenever you archive an image. Only the location(s) of the image have to be filled in. Nevertheless you'll be able to find your images more easily when you fill in as many of the fields possible.

When the given file location is not valid, you will be required to select another location. If the filetype of your image is "ICS" you will have to fill in also the 'Ids-location'. This is most of the time the same directory as the 'Location of the image'. Otherwise you only have to fill in the 'Location of the image'.

After you have filled in the image location and other input data, you can press the button Upload file and your image will be stored.

Exercises

Exercise 1: How to upload an image by making a new template.

In this exercise you will create a new template and archive the image "spiral32.ics". In the next one an existing template will be discussed.

It is not mandatory to fill in everything whenever you create a new template. Only the name of the template has to be filled in. Nevertheless you'll be able to find your picture more easily when you fill in as many of the fields possible.

1. First select the button upload from the menu on the left side of your computerscreen. The upload screen will appear.
2. Select for the type of the file ICS.
3. Select for template new template.
4. Press the Next button. An empty form will be shown. You just fill in this data in the concerning fields:
5. 'templatename': Test.
6. 'Position of the origin': 1.
7. 'Samplingdistance': 2.
8. 'Type sensor': 3.
9. 'Number of channels': 4.
10. 'Dimensions of the sensor': 5.
11. 'Wavelength of the excitation': 6.
12. 'Wavelength of the emission': 7.
13. 'Number of photons needed to excitate one colourmolecule': 8.
14. 'Refractionindex of the medium': 9.
15. 'Numerical aperture of the lense': 10.
16. 'Refractionindex of the medium for which the lens is designed': 11.
17. Click on the button Add template to add your template to the database. You will see the next page with your just added template and new fields.
18. Now you will have to fill in further information about your image: Click the button Browse to select the 'location of the image': spiral32.ics.
19. Click the button Browse to select the 'ids-location' of the image: spiral32.ids.
20. Fill in as 'Description': This is a testfile with 44 channels.
21. Check the box 'Private' to make your file only visible to yourself.
22. Click the Upload file-button to upload the image.

The locations of the image always have to be filled in! When the given file location is not valid, you will be required to select another location. 'Description' and 'Private' are not compulsory.

The following screen shows you that your file has been uploaded. Congratulations!

Exercise 2: How to upload an image using an existing template

In this exercise you will use an existing template to archive the image "faba64.ics".

1. First select the button upload from the menu on the left side of your computerscreen. The upload screen will appear.
2. Select for the type of the file ICS.
3. Select for template Test.
4. Press the Next-button. Now you will have to fill in further information about your image:
5. Click the button Browse to select the 'location of the image': faba64.ics.
6. Click the button Browse to select the 'ids-location' of the image: faba64.ids.
7. Fill in as 'Description': This is a testfile.
8. Don't check the box 'Private' to make your file visible to other members of your group.
9. The locations of the image always have to be filled in! When the given file location is not valid, you will be required to select another location. 'Description' and 'Private' are not compulsory.
10. You will see the next page with the data of your selected template Test and new fields.
11. 'templatename': Test.
12. 'Position of the origin': 1.
13. 'Samplingdistance': 2.
14. 'Type sensor': 3.
15. 'Number of channels': 4.
16. 'Dimensions of the sensor': 5.
17. 'Wavelength of the excitation': 6.
18. 'Wavelength of the emission': 7.
19. 'Number of photons needed to excitate one colourmolecule': 8.
20. 'Refractionindex of the medium': 9.
21. 'Numerical aperture of the lense': 10.
22. 'Refractionindex of the medium for which the lens is designed': 11.
23. It is possible to alter some of the data of your template. Fill in: 'Number of channels': 44. When you have done this the number '44' will be stored instead of '4'.
24. Click the Upload file-button to upload the image.

The following screen shows you that your file has been uploaded. Congratulations again!

Exercise 3: How to upload an image without using a template

In this exercise you will archive the image "66_spiral32-3ch.ics" without using a template.

1. First select the button upload from the menu on the left side of your computerscreen. The upload screen will appear.
2. Select for the type of the file ICS.
3. Select for No template.
4. Press the Next-button. A new screen will appear and you have to select te imagelocation. Now you will have to fill in further information about your image:
5. Click the button Browse to select the 'location of the image': 66_spiral32-3ch.ics.
6. Click the button Browse to select the 'ids-location' of the image: 66_spiral32-3ch.ids.
7. Fill in as 'Description': This is a testfile with 44 channels.
8. Check the box 'Private' to make your file only visible to yourself.

Next: Search in the archive