If you have integrated IceBear with your imaging system, plates will be imported automatically, along with their plate type, images, etc.
If you don't have imagers, or are working with plate formats that won't fit in your imagers, you will need to create a plate manually. From the main menu, select "Add a plate".
In the Barcode field, choose a unique identifier. You should avoid spaces or special characters and keep this as short as reasonably possible; it may end up in a filename somewhere.
Choose the correct project and plate type for your plate, then click Create. You will then see the new page for your plate.
You can navigate to the plate's project by clicking its name in the Details box, or by clicking the project icon in the top left.
The details box contains some basic information about the plate, including its barcode and plate type.
The plate's project is also shown. Click the project name to go to it. If this is "Default Project", you should assign it to a real working project. You can do this by assigning a protein to the plate in the Protein tab. Plates in the default project can only be seen by the plate owner.
The plate's owner is determined from the imaging system; in Formulatrix systems, this is done by matching the plate owner's email address in RockMaker to an IceBear user.
The plate importer may recognise some RockMaker "users" as defaults, that is, they indicate that the correct plate owner was not properly set in RockMaker. If you didn't set yourself as the plate owner in RockMaker, and the RockMaker default is recognised by the importer, IceBear will assign your plate to an "Unknown User"; only administrators will be able to see the plate and sort it out.
This tab shows all the times that the plate has been imaged. The imager and temperature for each imaging session are also shown.
The light bulb shows you what kind of imaging was done: A yellow bulb is visible light, and a purple bulb is UV.
Click on any date/time to go to the drop viewer and see the images. Most of the time, you'll want the most recent images, so click the one at the top.
You may have the option to add manual inspections to the plate. Click Create new manual inspection for this plate... to open the inspection form.
IceBear assumes that manually-added images are taken in visible light (as opposed to, say, UV). Specify the date/time, and which imaging device was used - typically "+4 Microscope" or "+20 Microscope". Then click the Create button.
Now, you can attach images to your new inspection.
For plates with more than one sub-well per well position, first click the correct drop number on the left.
Click the correct well for your image. You can then select the image to upload, and a thumbnail of it will appear in the well.
To remove an image that you have already uploaded, click it. Click OK when you are asked to confirm. The image will disappear.
If you have scale information for your image, you can enter it into IceBear. Doing this will let you use the Measure tool in the drop viewer. Right-click the image and enter the scale into the box that appears. Note that the unit is microns per pixel.
When you have finished uploading images, you can view the inspection in the Drop Viewer and mark crystals for onward processing.
Click the Edit... button beside the inspection. This works just like creating one.
The Crystals tab lists all associated crystals. For each crystal, the image, plate, and well, drop and crystal number are shown.
There is also a star rating beside each crystal; you can change this in the crystal's view page or in the drop viewer. The star rating is entirely subjective, so it's up to you what they mean. You can sort the list to bring the best-rated crystals to the top.
Click the image to open it in the Drop Viewer. Click the plate name to go to the plate. Click the well and drop details to go to the crystal page.
If you have already set the protein for this plate, you will see some basic information about it here.
You can also set the protein buffer and protein concentration.
If you have not set the protein, click the Choose... button. A box opens showing all the projects and proteins you can see:
Step down through the project and protein to locate the right construct. Click "Use this construct".
IceBear sets the construct into the relevant sub-well in all wells of the plate, and puts the plate into the construct's project. From here on, anyone with permissions on that project is able to see the plate in IceBear.
Once you have chosen the construct for one sub-position, you can copy it to the others or choose a different construct within the same project.
If you have already set the protein for this plate, you can change it, but only within the same project.
The Screen tab is where you give IceBear information about the crystallization conditions in your plate.
Note that you must set the protein and construct before you can enter screen information.
If the screen has not been set, you will have two choices. Either choose a standard screen already in IceBear, or upload details of an optimization screen.
IceBear can understand screen information in the .csv format output by Mimer. It also understands some XML formats. It will extract the conditions from the file, and attach the file to the plate in the Files tab. If your format is not supported, you can always upload the file directly into the Files tab.
After setting the screen, the Screen tab will look something like this:
The Drop Conditions tab lets you specify the volume of well and protein solution used in each position in your plate:
The layout of the drops within the well should look like the actual plate, and the numbering of the drops should correspond to the drop numbers in the imager. If this is not the case, ask your administrator to change the "drop mapping" for the plate type.
Here you can see attached files, and attach new files if you have permission.
Any attached files are listed along with a description and the file size. Click the filename to open the file in a new tab.
If you have permission to add files, simply select the file, give a short description, and click the Add file button.
Here you can read any notes that have been made, and make new ones if you have permission.
All notes are labelled with the date and time when they were added, as well as with the name of the author. You don't need to write these into your note.
You can tell IceBear that you have destroyed your plate. To do this, click the Destroy plate button.
This disables some functions, such as creating manual plate inspections. You can also see that the plate has been destroyed, so you don't waste time looking for it.