[[ https://imaris.oxinst.com/ | Imaris ]] is a closed source 3D visualization and segmentation software built by Bitplane, now part of Oxford Instruments. The BIOP boast two licenses for Imaris 9.5.1 with the following packages Vantage, Coloc, MeasurementPro, Track, XT. (WARNING) Packages not included in the BIOP licenses: Cell, Filament Tracer, Batch, ClearView, Stitcher = Converting to IMS formats = As of version 9.0, Imaris no longer natively opens formats other than IMS, but includes a file converter. Imaris can convert most microscopy formats (Zeiss, Leica, Olympus, ...). - When you start Imaris, it will open an "Arena" view. - From there ask it to "Observe a Folder" and add the folder with your data. - It should find all your images and when you double click on one, it will convert it to IMS first (this is quite fast). - You may need to refresh the folder view in order to see the newly created IMS file = Imaris Free Viewer = https://imaris.oxinst.com/imaris-viewer = Imaris First Time Setup = When launching Imaris for the first time, you need to make some initial adjustments. NOTE: As of Imaris 9.5.1 it complains a lot about licenses not being found. Keep clicking `OK` until it finishes complaining... == License Server Setup == 1. Click on the {nav icon=key, name=Key} icon (written Administrate) 2. Select **Define Floating License Server** |Servername | ptbioplicense.epfl.ch | | Port | 2700 | {F512625, layout=center} 2. Provide the amount of **Texture Cache Limit** which depends on the GPU of the machine | PC | GPU |RAM|Suggested| |----------------|-----------------|-----|----------| |Peacock Spider | RTX 2080 Ti | 11GB | 9600 | |Pink Panther | RTX 2080 Ti | 11GB | 9600 | |Mantis Shrimp| Quadro K5200 | 8GB | 7552| |Red Panda | GTX 580 | 2GB | 1750 | 3. Set The SWAP Folder Somewhere other than C:/ 1. Press {key CTRL P} to access the **Properties Menu** 2. Navigate to {nav Calculation} and change the **Cache File Path** to something like `D:\Swap` 4. Make sure that the XTensions folder points to the Matlab files 1. From the ** Properties Menu**, navigate to {nav Custom Tools} 2. Change **rtmatlab** to **matlab** {F14540449, width=400, layout=center} = TeamViewer = Please follow these instructions to connect via TeamViewer Use the following Connection Information ==Peacock Spider== 1 577 766 762 Password: biop-peacock == Pink Panther== 536 668 160 Password: pink-biop WARNING: This is experimental and not very safe. Please ensure you are the one who has booked the machine before trying to connect. And do not turn off team viewer at the end of the session. Just log off normally. == Mantis Shrimp and Red Panda == Mantis shrimp and Red Panda have a GPU that is compatible with Imaris remotely, so no TeamViewer is allowed. Request a normal Remote Desktop connection, see [[ bioimaging_and_optics_platform_biop/computers-servers/ ]] for more information. Red Panda can be setup if needed. Please get in touch with Oli. = Imaris Remote License Manager (RLM) = At the BIOP, we opted for a floating license approach to Imaris, as we have two full licenses and two basic licenses (Up to Imaris 7.6.1) and over 10 computers that could benefit from using Imaris. == ptbioplicense.epfl.ch == We requested a static IP address as well as an alias 'ptbioplicense.epfl.ch' to make connection to the license server as simple as possible. === Update 2019 === Our Intel NUC passed away and we requested a virtual machine through SV-IT and Oli installed everything. The machine is still accessible via 'ptbioplicense.epfl.ch' Issues with the machine should be adressed to [[mailto:paul.schalbetter@epfl.ch| Paul Schalbetter]] == In Case Of License Problems == Connect to **ptbioplicense.epfl.ch** using Remote Desktop Connection (You can use your BIOP credentials) {F512599, layout=center} Then open **Windows Services** by clicking on the Desktop shortcut and locate **Imaris Remote License Manager** {nav Right Click > **Restart**} {F512617, layout=center} === If the service stops right after being restarted === Try to kill the process `bitplane.exe` from the task manager before restarting the service. {F13798736} Eventually, you may have to start the `Task Manager` and `end task` of `bitplane`. == Changing the `bitplane.lic` and `bitplane.opt` Files == If we get new `bitplane.lic` and `bitplane.opt` these are the steps to change them 1. Remotely login to `ptbioplicense.epfl.ch` 2. Go to **Services** and stop the **BitplaneRLM** Service 3. Go to C:\rlm and copy the old `bitplane.lic` and `bitplane.opt` files somewhere safe, rename them. 4. Copy the new `bitplane.lic` and `bitplane.opt` files into the rlm folder. 5. Restart the **BitplaneRLM** Service