Organizer - Moving slides and folders
Organizer - Folder administration
Check for new slides
Upload slides


In the Slide manager slides and snapshots can be uploaded, indexed, and archived in a customizable folder tree. As can be seen from the Tab headings below in Figure 1, the Slide manager is divided into three sections corresponding to these functions.

In the Organizer tab slides can be archived in custom folders, diagnosed with indexed topography and snomed-M codes, renamed, annotated and previewed. Technical info can be edited.

In the Check for new tab new slides and snapshots on the server can be detected, and selected for archiving or discarded.

In the Upload slides tab slided and snapshots can be uploaded with a ordinary web browser, and automatically indexed after upload.

Fig 1. The Organizer tab in the Slide manager.

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When you open the Slide manager the default tab is the Organizer. The basis of the Organizer is the "Folder tree" on the left side (see Fig 1), with a Root folder on the top level. Under the Root folder you can have any number of subfolders which in turn can contain their subfolders. The last folder is the Recycle bin (Fig 1), containing recently deleted slides, snapshots or folders. Please note that each administrator has his own Organizer folder structure, not seen by anyone else.

Up on the right side of the Organizer is the caption of the currently selected folder ("Root" in Fig 1). Below the caption, a collection of command links can be found (see below), and below the command links the slides and images archived in the currently selected folder are listed in a slide table.

Above each column in the slide table is a link. The "All" link will select all the listed slides and snapshots, while the other links will set the sort order to either "Caption", "Type", or "Date".

By entering a search term in the Filter textbox, and clicking the "Filter button" (Fig 1), you can list only the slides you are interested in.

By holding the cursor over the small thumbnail of a slide, a larger preview is shown in the browser. By clicking the thumbnail the slide or snapshot is opened in the viewing window. By clicking the blue slide caption link, the current row is expanded to show more info on the slide or snapshot, a larger preview, and a link to edit the slide info (Fig 2).

Fig 2. One row is expanded in the listing of slides and snapshots in the Organizer.

Clicking the "Edit info" link in the expanded row (Fig 2) opens up the slide information view (Fig 3), temporarily hiding the other slides in the folder. On the top half ("Indexing information") you can edit the caption of the slide, add indexed and freetext diagnoses and a description of the slide or snapshot. When you add the slide to a slide page this information is copied to the page.

On the lower half of the page you can see and also edit the Technical information of the slide or snapshot (Fig 3). The pixel size is important as the zooming in the viewer scales accordingly. The pixelsize is entered in nanometers. Please remember to click the "Save changes" button to commit the changes.
Fig 3. The 'Edit info' view in the Organizer. In the upper half of the view diagnostical
information is entered, while technical info is enetered below.

Topographical information about the slide is entered in 3 levels ("Topography lvl 1-3" in Fig 4). After selecting the first level, the dropdown with the second level organds will be filled and selectable (Fig 5). Please remember to press the "Save changes" button after selecting.

Fig 4. The first level of Topography is selected.

Fig 5. The second level of Topography is selected.

Morphological information about the slide can be indexed by writing 4 characters contained in the diagnosis (numbers or text), and then selecting one of the suggested diagnoses (Fig 6). Freetext can also be added in the field.

Fig 6. Morphological info about the slide. In this example 'carc' is entered in the textbox, and the server lists all diagnoses containing this character sequence.

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Organizer - Moving slides and folders

Slides and snapshots  can be moved to another location in the Organizer by first selecting them to the left in the slide listing (Fig 7), and then clicking the "Move to another folder" link above the slide listing. When this link is clicked you will see a thumbnail listing of the slides that will be moved, and a "Confirm move slides" button. When you have selected the destination folder in the folder tree to the left, you can click the "Confirm move slides" button and the slides will be moved.

Folders are moved in a similar manner, except that the "This folder: Move" linkbutton should be clicked to move the currently selected folder.

Fig 7. To move slides and snapshots, first select them by adding a mark in the checkboxes of the slide listing.

Fig 8. When the destination folder is selected in the folder tree, the slides are moved by clicking the 'Confirm move slides' button.

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Organizer - Folder administration

There are 3 main command links to administer folders: Move, Rename amd Add subfolder (Fig 9). For the Move command, please see "Organizer - Moving slides and folders". If you click the "Add subfolder" command link, a new subfolder to the current will be created. The default caption of a new subfolder is "New folder".

Fig 9. The 3 main command links for folders.

Folders in the Organizer can be renamed by clicking the "Rename" link above the slide listing. Also a description (for own purposes) can be added. Changes are committed by pressing the "Update folder" button. You can return to the Orgnizer slide listing by clicking the "Close edit folder view" button.

Fig 10. The folder edit view.

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Check for new slides

Slides and snapshots which are added to the server other ways (for example via the LAN, USB etc) than through the integrated upload function (see below) can be indexed for use on the portal in the "Check for new" tab in the Slide manager. When the tab is opened a check for newly added slides will be performed. If new files are found, you can choose to index them all automatically, or manually (Figure 11).

If you click the "Index all for me" button (Automatic indexing), the new slides will be added to the Root folder in the Organizer of the Slide manager.

Fig 11. The Check for new tab.

If you click the "Manual indexing" button (Fig 11), files not yet indexed will be listed in a table (Fig 12). The list of unindexed slides and snapshots can be sorted according to Name, Date, Type or File size, and if you have more than one server folder defined you can select which folder, or all, to search for new slides. You can also filter the table by File type, or by a search term.

Fig 12. Manual indexing of slides.

To the left in the list of unindexed files is the file name as appearing on the server. For each file then follows three selectable buttons: "Index", "Ignore" and "Cancel". By selecting "Index" a slide or snapshot will be added to the Root folder in the Slide manager. If you select "Ignore", the slide will be hidden in subsequent searches for new slides. Selecting "Cancel" means that no action will be performed for the slide. Please note that you do not have to select any of the options, meaning the same as "Cancel". From a long list you can select only the slides you wish to index, and then press the "Commit changes" button.

If you have previosly selected "Ignore" for some slide you now wish to index you can select the "Show ignored" checkbox on the right side.

Fig 13. Manual indexing of slides.

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Upload slides

Slides and snapshots can be uploaded and automatically indexed by selecting the "Upload slides" tab in the Slide manager (Fig 14). You can select which folder the files are uploaded to in the "Server folder" dropdown control. The uploaded slides will be indexed with the settings (pixel size, scanner tag) of the selected server folder, but you can edit these settings later if you whish to.

To upload slides, you can either click the blue "Upload Filee" button, which will open a select files dialog on your computer, or, you can drag and drop files on the "Drop Files" area. Currently supported file formats are jpg and png for snapshots, and ECW (Enhanced Compressed Wavelets) and jp2 (jpg2000) for virtual slides.

Fig 14. The Upload slides tab.

Please note that on slow servers the preferred slide format is ECW, while on fast servers jp2 files will decompress fast enough. Please also note that jp2/jpg2000 files can be compressed with a variety of parameter settings, which may not be compatible with the WebMicroscope administration and viewing systems. Please contact us on compatibility issues.

Once you have selected, or dropped, the files you wish to upload, proceed by clicking the blue Upload button (Fig 15.).

Note: When you have uploaded new slides, go to the Check for new function to index the new slides.
Please note that it might take up to 100 seconds before virtual slides are visible on the server after upload.

Fig 15. Uploading slides.

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