wiki:FAQ
Last modified 4 years ago Last modified on 04/30/15 11:45:27

Brain Slices - Frequently Asked Questions

  1. General
    1. What is it for?
  2. Usage
    1. I have loaded images to the image cart but I am unable to see them. How can I see them?
    2. How to visualize uploaded slices?
    3. How can I create a new filter?
  3. Troubleshooting
    1. There is some issue (and my browser is neither Chrome nor Chromium).
    2. Why does my pixel size/resolution/offset given on upload is ignored (and so are properties of floating point number type)?
    3. I have annotated my images with properties that are numbers (e.g. age, thickness, weight, z coordinate...) but they are not matched by related numeric filter.
  4. Doubts about interface behaviour
    1. In the upload section change of the unit is automatically changing the value in the number fields - is that intended?
    2. Is quality setting working? I can see no difference between High and Medium (or Low and Medium)

General

What is it for?

The service is for storing, browsing, sharing and publishing of high-resolution images of brain tissue with detailed description.

With BrainSlices you can share your images with collaborators all around the globe as well as you can refer to them (images, not collaborators) as supplementary materials thanks to their permanent URLs.

Usage

I have loaded images to the image cart but I am unable to see them. How can I see them?

  1. Open the image cart (cart button is located in the right side of the top bar).
  2. Switch the service into visualisation mode (third button from left on the top bar).
  3. Check checkboxes by the images you want to view in the field (left of the image cart).

If you are still unable to see anything:

  1. Focus (focus widget is on the top bar) on the expected location of the image.
  2. Try to zoom out (to 1x with zoom widget on the top bar or even smaller value with your mouse wheel).

If it still does not help, that means that probably the image uploader has screwed something up with image metadata. Contact him or her if possible.

How to visualize uploaded slices?

  1. Wait some time (the server needs it to process your images).
  2. Login to the account the images were uploaded (if not already logged).
  3. Switch to the “browse” mode (second button in the top bar).
  4. Remove every filter you have created.
  5. Select “My images to be accepted”.
  6. Optionally you can select collection your images have been uploaded as (or into)
  7. Click [Apply filters] button.
  8. Your images shall appear in the results. You can accept, adjust and annotate them after adding them to the image cart. You can also grant puplic privileges there.
  9. If some of your images are missing - wait a bit longer. It might be that the server has not processed them yet.

Also see the answer I have loaded images to the image cart but I am unable to see them. How can I see them? for visualisation issues.

How can I create a new filter?

  1. Enter a name of the property to be filtered. You can also select “--- any property ---” option.
  2. Select type of search (available options are dependent on the properties available in the database):
    • tag - matches any property of given name,
    • number - matches numeric (integer or float) properties within given range,
    • text - matches text properties (text, string or enumerative) in natural English language,
    • enumerative - matches enumerated set of property values.
  3. Select details of match (unless tag type is selected).
  4. Click “add” (“+”) button.
  5. A new filter is appended to the list. You can now either change match details or delete the filter.

Troubleshooting

There is some issue (and my browser is neither Chrome nor Chromium).

Install either Chrome (https://support.google.com/chrome/answer/95346) or Chromium (package chromium-browser for Ubuntu) browser and try again. Chrome and Chromium are the only browsers we guarantee to be supported by the service.

Why does my pixel size/resolution/offset given on upload is ignored (and so are properties of floating point number type)?

It might be an issue of your locale with comma (“,”) used as a decimal point. Browsers might be not recognizing it as an numeric input. Please use full stop (“.”) instead.

I have annotated my images with properties that are numbers (e.g. age, thickness, weight, z coordinate...) but they are not matched by related numeric filter.

If images are not accepted yet, assure that “My images to be accepted” filter is selected rather than “images I can view”. Assure that you have selected a numeric (integer or float) type for the properties.

Doubts about interface behaviour

In the upload section change of the unit is automatically changing the value in the number fields - is that intended?

Yes, it is.

Is quality setting working? I can see no difference between High and Medium (or Low and Medium)

Yes, it is working.

The image at server-side is stored prescaled to certain zoom values. If requested zoom value is none of them, the image has to be rescaled at client-side. When high quality is chosen, the image of the nearest greater zoom value (more details but also more data to transfer) is chosen to be downsampled. When low quality is chosen, the image of the nearest lower zoom (less data to transfer but also less details) is chosen to be upsampled. When medium quality is chosen, the image of the nearest zoom is chosen (so one time it is low and other time high quality).