VIRMISCO is a virtual microscope that offers virtual access to collections and research objects while conserving the originals, e.g. type material. The VIRMISCO search and viewer are freely accessible via the internet and the software is open-source. It can be used with almost every browser, but has been optimized for Mozilla Firefox (-v. 45.2) and Microsoft Internet Explorer ( v. X). To facilitate a comfortable start in the use of the VIRMISCO search and viewer, this quick-guidance manual describes its functions and use.
The Full-text search offers a quick search for all terms connected to the object, e.g. taxon name, type status, photographed part of animal, country, province and date. The full-text search accepts only complete words (Lasioseius, not Lasios!). Enter one or multiple search words and then click Search on the right side of the input field. Multiple search words will not filter for all terms entered but providing all objects containing at least one of the entered terms. Entering no search term will result in a list of all objects available in VIRMISCO.
The Advanced search provides an opportunity for filtering or specifying the search. Location and taxon is hierarchically structured (Country – Province - Region -Place; Higher taxon - Genus - Species). Select from the respective lists of the available digitalized objects. For searching by sampling date (on/after and/or before), enter the date using the format YYYY-MM-DD or the pop-up calendar by clicking on the symbol on the right side of the input field. After specifying the advanced search click on Search on the lower right side to see the results.
The user interface for selecting digital photomicrographs is split into three parts.
1. Select a photomicrograph
Taxa are listed under the valid taxon name written in bold face. Click on an object to get more information.
See chapter “How to read the name of an image stack?” below for an explanation of the object or file name.
2. Drag the preview image down to the selection box
In the upper field of the information box are the higher taxon hierarchy, scientific name and valid name provided. In the lower field „Properties matching search criteria“ matched terms are highlighted in bold face. Under the information box is an overview photograph of the specimen given on the right hand side. The location where the photomicrograph was taken is indicated by a colored dot. On the left hand side a small preview of the photomicrograph is shown. To select an object to show in the viewer click on the left image and keep the left mouse button pushed, then pull it into the grey items box below (drag & drop). You can drag several photographs from several species.
3. Reorder items or drag them to the trash bin
The dragged photomicrographs are shown as a preview in the box with the name of the image stack. You can reorder them by drag and drop (left side first) or you can delete images from the selection by dragging them to the bin symbol on the left hand side. To show your selected photomicrographs in the viewer click on Show in viewer on the right hand side of the items box.
Important information on the image stack names and standards used in Acari
How to read the name of an image stack?
Every image stack name has the same standardized system to be named:
genus_species_type status[abbr. HT=holotype; PT=paratype]_sex-[abbr. f=female; m= male; DN=deutonymph]_part of the body [leg number in Roman numerals; abbr. le=left “side of specimen”; ri=right ”side of specimen”]_specific (collection) number of the microscope slide_date when photograph was taken or uploaded [format DD.MM.YYYY].
Halolaelaps_antarcticus_HT_f_leg II ri_90.35512_20.05.2016
= Halolaelaps antarcticus, holotype, female, leg pair two on the “right side of the specimen”, carrier number 90.35512, photomicrographs
taken/uploaded at 20th May 2016
Acari: Orientation of specimen
All specimens of mites were photographed with head/anterior body directed to the left side.
Acari: “Side of specimen” on the microscope slide viewed
Important: This is not the natural side or half of body of the specimen!!! The specimen and its neighboring area is (imaginary) divided into the right and left side by a longitudinal axis seen through the microscope, which is not necessary to be equal with the natural half of body. You could also say left/right side of longitudinal axis of the specimen (see example figure below). Often there are broken or loose parts of the body, where the actual view and natural orientation is not known or time-consuming to be find out. Also in very flat specimens, e.g. mites, it is not easy to decide whether you look on the dorsal or ventral side of the animal. The position left or right to the longitudinal axis of the specimen on the microscope slide is therefore more important than the natural position or view.
The Viewer – The virtual microscope
The VIRMISCO viewer displays the photomicrographs like in a real microscope.
The viewer window shows the movie file from the photomicrographs or the selected focal plane. By clicking on the image and keep the left mouse button pushed you can drag the photomicrograph movie within the viewer.
List of selected photomicrograph
You will find a list of all selected items on the upper right hand of the viewer window. The currently shown item in the viewer is marked in green. If more than five items are in the list a scroll bar is available on the right hand side to scroll up and down.
Information on the shown photomicroslide
On the right hand side information and meta data on the photomicrographs is provided, e.g. microscope slide, gathering, as well as on the settings, microscope and the camera used for the photomicrographs. Below the Photomicrograph at direct link to the image is provided. Below the latter downloads of the currently selected image stack are provided as 1) a compressed ZIP Archive (JPEG files); 2) a video Ogg/Theora file or as 3) a video H.264/MPEG-4 AVC file.
To set the viewer and photomicrographs to your individual requirements several settings via scroll bars are provided.
- Rotation: Rotate the image left or right up to 180°.
- Zoom: Zoom in (max. 10x) or out (max. 0.1x).
- Buttons: [<<] go to the first focal plane and stop; [|<] go one focal plane further and stop; [II] pause; [>I] go one focal plane back and stop; [>>] go to the last focal plane and stop; [I<=>I] start video.
- Playback rate: Speed of photomicrograph video shown (max. 2x).
- Loop begin: Select at which focal plane the loop begins.
- Focal plane: Select any focal plane. Currently viewed focal plane number is shown.
- Loop end: Select at which focal plane the loop ends.
- Brightness: Adjust brightness from dark (left) to bright (right). Only works when viewer paused [II] for a single focal plane!
- Contrast: Adjust contrast from low (left) to high (right). Only works when paused [II] for a single focal plane!
Save a single focal plane image.
- Current region: After clicking the current image appears on the screen with the selected settings. Right-click on the image and choose to save it or left-click anywhere on the screen to go back to the viewer.
- Whole image (frame): After clicking the current whole image appears on the screen with the selected settings, except rotation and zoom. Right-click on the image and choose to save it or left-click anywhere on the screen to go back to the viewer.
Measure a region, e.g. tarsus or chaeta.
Left-click set begin. Choose any spot on any focal plane and click the left mouse button for setting first measuring point. Then choose another spot on any focal plane and left-click for setting second measuring point. Then, the total distance (∆true) between the two measuring points is shown in the viewer. Other values are available in a box below set begin. Click Clear to clear values for another measuring.
- ∆x: Value of X-coordinate (= vertical direction)
- ∆y: Value of Y-coordinate (= horizontal direction)
- ∆z: Value of Z-coordinate (= height direction)
- ∆proj: Projected value of X and Y-coordinates.
- ∆true: True value of X, Y, and Z-coordinates.