MANUAL UNDER CONSTRUCTION

Welcome mode

The BrainSlices website starts in a welcome mode displaying introductory information.

Toolbar

In the top part of the site you can find a toolbar containing the following buttons (from left to right):

• mode switching buttons (the button of the active mode is highlighted):
  • Home button for the welcome mode,
  • Browse button for a browse mode,
  • Visualise button for a visualise mode,
• image cart button,
• help button,
• login button.

Additional mode-specific buttons are described in the mode-related section of this manual.

Browse mode

To browse images go to the browse mode (click the "browse" button in the toolbar). You will be able to browse all your images as well as the images of other users, that were made publically available.

The view of the browse mode consists of two panels: A pair of panels would appear: the "Filters" panel (1 - the smaller red rectangle) and the "Search results" panel (2 - the bigger red rectangle). In the exemplary "Search result" panel you can see a list of several specimens. The visibility of the "Filter" panel can be controlled with either a button in the toolbar (3) or an expand widget (4).

"Search results" panel

The major part of the panel is a list of search results (1 - the big red rectangle), which every item (2 - the small red rectangle) represents a specimen found. The total number of found specimens is displayed in the header of the list (3). If the list is too long to fit in browser's window, a scrollbar (4) will appear. If more than 50 specimens are found, the list will be paginated and a pagination widget will appear in its header (3).

Every item in the list contains of a thumbnail image (5) and a detailed description of the specimen. Specimens might be characterized by many properties (6; e.g. method of staining, species, plane, etc.). Additionally, they may be tagged with a keyword (7; e.g. mouse, nissl, etc.). Images might also be named (8) and provided with an informal description (9).
Tags, names and informal description are further considered to be properties, too (e.g. when filtering images).

If the description of a specimen is too long to be fully visible, an unfold/fold (10/11) widget appears.

There are two icons in the top-right corner of the item. To download a PNG file (containing the original bitmap of the specimen's image) click the download icon (1). To add the specimen to the image cart click the "+" ("add to the image cart") icon (2).

Filter panel

A new filter panel is unfolded by default.	To fold it click on its title (1).

In order to create a new search filter go to the "New filter" panel (1), choose a name of the filtered property (2) and its type (3) as well as the filter’s details (4).

You can also select --- any property --- (2). Then the matching phrase or number will be searched in all properties. If the filter type is set to Tag - all images with any description will be found.

After the new filter is configured, click on the "+" icon (5) to create it.

A new filter is folded by default.	Click on it to unfold.

In order to remove the filter, click on the "x" icon (6).

To search the repository choose an appropriate set of filters and click on the "Apply filters" button (7). You can limit the number of the search results (8). You can also limit the search with regard to your privileges (as an owner, editor, annotator or guest; 9).

Filter types

Since properties describing a specimen might be of various type, there are several types of filters available.

Text filter

A new filter panel.	Panel of an existing filter.

Every property (e.g. thickness) might be interpreted as a text in a natural-language, so you can search for it with text filter.

Numeric filter

A new filter panel.	Panel of an existing filter.

Some of properties (e.g. thickness in μm, age of the animal in days etc.) are numeric values. A numeric filter allows to constrain them.

Specification of an upper bound (or equality) constraint.	Specification of a lower bound constraint.

Tag filter

A new filter panel.	Panel of an existing filter for a particular property (top) and any property (bottom).

To search for images either tagged with a particular keyword or described with property of particular name use the tag filter. To search images with any description use tag filter for --- any property ---.

Enumerative filter

A new filter panel.	Panel of an existing filter.

Some properties (such as sex or staining method) might be searched by selecting a set of enumerated values (like male and female for sex). For that purpose use the enumerative filter.

Image cart

A concept of the image cart is similar to e-commercial concept of a ​shopping cart and allows users to accumulate a set of images.

The image cart (1) can be opened/closed with either the "image cart" button in the toolbar (2) or the expand widget (3).

Adding images

In order to add a particular specimen to the cart, you might either drag'n'drop or double click the appropriate item in the search results list. You might also click "add to the image cart" icon (4). Note that if the specimen is already in the cart, its "add to the image cart" icon (5) is grayed out to indicate it is disabled.

To add all the specimens from the search results at once, click the "merge into the image cart" button (6). All the images already in the cart will stay there (but will not be duplicated). To replace the current content of the cart with search results click "replace the image cart" button (7).

Image cart panel

The main part of the image cart panel is a list of its content (1), similar to the list of search results. Note, that "add to the image cart" icon of every item has been replaced with "remove from the cart" icon (2). There is also an additional panel (the "Loaded" panel; 3) placed on the right side of the item (the panel is discussed further in the visualise mode section). In contrast to the "Search results" panel, there is no pagination and the order of items can be changed by drag'n'drop technique.

To perform any operation (e.g. fold/unfold item, load image into visualisation field etc.) on every specimen in the image cart use the "Apply to all" subpanel located in the panel's footer (4). The subpanel contains "fold all"/"unfold all" widget (5). More operations - available after clicking "more options" (6) - are discussed further.

In the panel's header (7) you can find "empty the image cart" button (8) and a widget controlling the order of the items in the cart (9). You can sort the images with respect to a chosen property.

Selection of the sorting property. Numbers indicate how many specimens in the cart have the property.	Selection of either ascending or descending order.

Visualise mode

To view images stored in the image cart switch to the visualise mode ("Visualise" button in a toolbar).

A display lattice (1 - the big red rectangle) will appear. The lattice may be composed of one or more display fields (2 - the medium red rectangle) depending on the chosen size. There might be an arbitrary number (at least one) of display fields.

The fields are numbered in  in left-to-right (primary) and top-to-down (secondary) order. The same image might be loaded into multiple display fields. You may also load an unlimited number of images into a single display field. In case of overlapping images you can adjust their transparency.

A scale bar (3) is displayed in the bottom right corner of every field. Next to the scale bar of the active field (the one under mouse pointer) the mouse pointer's location (4) is displayed in a coordinate system. All display fields share a common coordinate system. In any inactive field an auxiliary pointer (5) marks exactly the same point as mouse pointer in the active field.

Loading images into display field

You can load an image into a display field by either dragging it from the image cart or selecting an appropriate checkbox in the "Loaded" panel (7). Note that the arrangement of the checkboxes corresponds to the arrangement of the display fields. For instance, if the top left checkbox is selected, the image is loaded into the top left display field.

You might think about the loaded images as a stack of semi-transparent slides (layers), ordered from the top to the bottom layer of the display field in accordance to their order in the image cart. That way all of them might be visible even if they are overlapping (depending on the [#changingTransparancySettings transparency settings]).
Note, that the image at the bottom is always opaque.

To unload the image clear the appropriate checkbox. A removal of the image from the "image cart" implies unloading it from every display field it has been loaded to.

Toolbar of the visualisation mode (6)

Controlling dimensions of the display fields’ lattice

To change the number of rows and columns of the display fields’ lattice click the "display lattice dimensions" button and hold the left mouse button. An adjustable schematic lattice will appear. Adjust its dimensions and release the left mouse button. The display will be rearranged.

Note, that if the new display fields’ lattice consists of a lesser number of display fields than the old one, the display fields that are at the end (in left-to-right, top-to-down order) will be discarded.

Switching the display mode

With the "display mode" button you can switch between the filmstrip and the lattice display mode

Lattice display mode

All display fields are visible thus their size is limited.

Filmstrip display mode

The display fields’  lattice might be moved horizontally with a scrollbar (1). In this mode display fields might be bigger thus most of them might not fit to the window.

Unlinking display fields

The display fields are linked by default. The content of the linked fields moves and scales simultaneously when grabbed or zoomed. You can unlink them (and link them back) by pressing "fields linking" button.

Merging display fields

You can easily merge all display fields into one by using the "merge fields" button. All the images that have been loaded to the individual fields will be displayed in one display field.

Scattering images into separate display fields

With the "scatter specimens" button you can scatter all images loaded into display fields into separated display fields (in the image cart order). If an image is loaded into multiple display fields, after scattering it will be loaded into a single field.

Changing resolution of display fields

With the "global zoom" button you can open a widget allowing you to set resolution of all display fields by either entering a numeric value of the zoom factor or manipulating a slider.

You can also scale display fields with a scroll wheel of your mouse.

Changing transparency of stacked images

With the "transparency" button you can open a slider allowing you to change transparency of all stacked images but the bottom one (within a display field).

Focusing fields at precise location

To change the position of the focal point (the center) of display fields you can not only by dragging them, but also by clicking the "focus" button and providing a precise focal point’s coordinates in the opened widget.
Note, that a variety of units is available.

Changing quality of displayed images

To select quality of displayed images click the "quality" button. A group of buttons will appear, each corresponding to one of the quality settings:

• "High" - click it for the most detailed images,
• "Low" - click it for the most efficient image transfer,
• "Medium" - click it for a reasonable trade-off between image

quality and data transfer efficiency.

Note that the quality settings apply only to the images displayed in the display fields, but not to the PNG images available for download.