Dear Colleagues,
To bridge the time that our booking system (PPMS) is offline – and to plan and mediate services that become available – we provide this page as a temporary solution to request the services that become available again. Please use these “IOF services requests forms” for any service request. We ask you to only use email with specific questions.
To be able to access the IOF service registration forms, one needs to be on ISTA campus and logged in.
AVAILABLE SYSTEMS
We are working vividly to make the most systems available again and has priority above individual services, for which we will need to ask your understanding. Please also be aware that some systems services require a Service or Booking form to be filled out, and need a confirmation by IOF staff.
Available Systems
We will add systems to the list here as they become available
00. Slide scanner service: Zeiss Axioscan Z1 → Service request form → PPMS
00. Cytometry: Cytoflex LX; Sony SH800; Aria III → Service Request Form → PPMS
01. Widefield: Nikon Ti2E-01; Nikon Ti2E-02; Nikon Ti2E-03-PRIMO; Zeiss Axioscop; Zeiss Examiner D1NEW
02. Confocal: Leica SP8inv; Leica SP8up; Leica Stellaris 5; Zeiss LSM800-01inv; Zeiss LSM800-02up; Zeiss LSM800-03inv; Zeiss LSM800-04inv; Zeiss LSM800-05vert; LSM800-06vert; Zeiss LSM880up; Zeiss LSM880inv; Zeiss LSM900-01up;
03. Multi Photon: Leica sp8 DIVE → Booking Request Form → PPMS (required ≥ 48h before use)
04. Spinning Disk: Nikon CSU-W1-02; Nikon CSU-W1-03
05. Multi-Modal: Andor DF505;
06. TIRF: Olympus TIRF; Visitron iLAS
07. Light Sheet: Zeiss Lightsheet 7
08. Force Probing: to be announced shortly
09. Stereo Microscopes: Leica Stereo BFB (no cam); Olympus Stereo BFB (+Camera); Olympus Stereo LBE (+Camera); Bioluminescence Box;
Please be aware that it is likely that we will not be able to retrieve the functionality of all devices, especially systems running on older operating systems (XP / Windows 7).
Available Image Analysis Workstations
Analysis Workstations: we managed to resurrect 4 on-site workstations. Deployment of remaining Analysis Workstations depends on critical IT infrastructure (VPN, Remote Desktop Protocols), and can only be done after these critical IT infrastructure functions are available again.
- Analysis Workstations 4, 5, 6 (I01.O3.052a)
- Analysis Workstation 7 (I01.O3.052b)
All workstations are deployed with the same software: Imaris 9.9, Huygens 22.10., Ilastik 1.3.3pos3, CellPose 2, Fiji, Matlab and NIS viewer. Remaining software is currently not available. (Do not activate any update site, as it might break the current FIJI installation → inform us ; use the email tag “ANALYSIS”).
Rules & Guidelines
- BOOKINGS: As this resource is highly limited, please be considerate of others. We ask you to stick to a rule of maximum 3 hours of booking time during prime time (09:00 – 18:00).
- Logging on: The workstations are currently handled as local users, and can thus only by used on ISTA campus. Please mount your drives to retrieve your data (IT pages) and unmount them after your session!
- DATA handling: Transfer your analyzed data via Seafile ONLY (file size limit of 4GB). The use of USB data carriers is not allowed!
HPC Cluster:
IOF teamed up with Scientific Computing to make the HPC cluster available for image analysis.
- FIJI/Huygens is available on the cluster after training from the Scientific Computing unit.
REQUEST IOF SERVICES
The following available services required support from IOF staff. Please fill out the form 2 working days before intended use. We will do our best to keep up with the demand but please keep in mind that, it might take some time to organize. Requested service require a confirmation by IOF staff to ensure that staff is available.
Request Form Slide Scanner Service
- For questions about slide scanning service write to IOF@ist.ac.at, with ‘tag’ “SLIDESCANNER”
- For requesting the service, please fill out the form below
please use the PPMS request form
Request Form Cytometry Service
All Cytometry Services are to be requested or booked using the PPMS booking platform.
Confirmed bookings Cytoflex Analyser:
Cytoflex PPMS Calendar
Confirmed bookings Sony SH800:
Sony SH800 Calendar
Confirmed bookings Aria:
BOOKING REQUEST Level 3 Equipment:
IOF machine-park exists of differ
ent imaging technologies and applications, which also come with different levels of complexity. To clarify the complexity of the different systems, we indicate the level of complexity – and the default required training effort. The Leica DIVE (and Zeiss Lightsheet 7) are Level 3 systems and required IOF support for start-up →
Equipment Level details
Request booking in PPMS booking platform
Please see our “trainings materials” on our training page. Additional materials are shared on our ” training resource page” to additional information
ALL trainings are to be requested in the PPMS booking platform
IOF retrieval of Acquired Data & Infrastructure:
IOF has been intensely been collaborating with IT in the past year on the establishment of a new data infrastructure. Newly Acquired data will be synchronized continuously to a central server from IOF system computers (microscopes / cytometers), even while your are running your experiments. It is of importance to store your data in the designated storage location on the system computer. Your data will be ‘directly’ available and sorted by group and microscope. Acquired data will need to be moved to your own (or group) file service for processing and analysis!
Data retrieval
Newly acquired data retrieval: The data synchronization is planned to work as of week 50Older data retrieval: The data that was stored on IOF equipment is stored on external hard drives for now and is currently being scanned. The distribution of ‘safe/clean’ will likely be mitigated via our new data infrastructure (“Scratch4”), when this becomes available.- USB drives: No USB data carriers are allowed on any IOF equipment → unauthorized use will be seen as a serious offense as it can inject malware into our new infrastructure, thereby risking another facility shutdown.
Email tags: For inquiries about the services listed above, we ask you to use the following ‘ email title tags’:
- SLIDESCANNER: inquiries about slide scanner service
- ANALYSIS: questions about image analysis services
- FACS: inquiries about FACS service
- CLUSTER: inquiries about basic organization to use the HPC cluster
- TRAINING: please fill out the request form; otherwise use the tag in email communications
