Bioimaging Wiki

Dear (name of user),

My name is (name of team member) and I am a member of the GIMM Bioimaging Platform @ Lisbon Site, where you have asked for access to the (name of system).

Once you have read through this email, please proceed to filling the following form, which will give us more information about you and your experiment (https://forms.office.com/e/HJbF322YQn). If you are unsure on how to fill this form, come and talk with us, and we can fill it together.

You can find the [Lisbon Site] Bioimaging Platform in Room P3-A-5 (floor 3). Together we can further discuss your experiment, help choose the ideal microscope/technique, and book your first session.

Booking for training and imaging sessions is done through Agendo, and it is only possible if you already have an Agendo account. You will need to request access to the equipment, by clicking on the “keylock” icon on the top left corner, and request access to the system you require. A guide on how to register and use agendo can be found here (https://agendo.atlassian.net/servicedesk/customer/portal/2/article/668041217).

Trainings and acquisitions are done with your own samples, so please plan in advance to have it ready on the day of the 1st session. If your experiment is live, we might ask that your first training is with a fixed version to avoid time constraints. This allows us to understand your specific needs and sample characteristics, and adapt the training accordingly. Even if you already have experience, we can often provide suggestions that will improve your workflow and results.

If you anticipate needing substantial help with the protocol design, sample preparation, image acquisition or data analysis/figure preparation, please make sure to inform your PI that we must have a meeting to discuss this upfront.

Lastly, you can join our Microsoft Teams channel, where you can find all our announcements, a discussion chat, and our weekly “Tip of the Week” on image acquisition, analysis and data management, by following this link (https://teams.microsoft.com/l/team/19%3A85HZ7mBzO9MkHfY5T3Ns1qK1KTQC0-skSL1tQDEg6K81%40thread.tacv2/conversations?groupId=f70a1c00-51cd-4607-97ed-52b548ba3821&tenantId=09839d39-20e6-405d-8c08-dbc5e1ab3b3b).

Welcome to the Bioimaging Platform!

Dear (name of user),

My name is (name of team member) and I am a member of the GIMM Bioimaging Platform @ Oeiras Site, where you have asked for access to the (name of system).

Once you have read through this email, please proceed to filling the following form, which will give us more information about you and your experiment (https://forms.office.com/e/HJbF322YQn). If you are unsure on how to fill this form, come and talk with us, and we can fill it together.

You can find the [Oeiras Site] Bioimaging Platform on the Bartolomeu Dias wing (floor 0 of the main building). Together we can further discuss your experiment, help choose the ideal microscope/technique, and book your first session.

Booking for training and imaging sessions is done through Agendo, and it is only possible if you already have an Agendo account. You will need to request access to the equipment, by clicking on the “keylock” icon on the top left corner, and request access to the system you require. A guide on how to register and use agendo can be found here (https://agendo.atlassian.net/servicedesk/customer/portal/2/article/668041217).

Trainings and acquisitions are done with your own samples, so please plan in advance to have it ready on the day of the 1st session. If your experiment is live, we might ask that your first training is with a fixed version to avoid time constraints. This allows us to understand your specific needs and sample characteristics, and adapt the training accordingly. Even if you already have experience, we can often provide suggestions that will improve your workflow and results.

If you anticipate needing substantial help with the protocol design, sample preparation, image acquisition or data analysis/figure preparation, please make sure to inform your PI that we must have a meeting to discuss this upfront.

Lastly, you can join our Microsoft Teams channel, where you can find all our announcements, a discussion chat, and our weekly “Tip of the Week” on image acquisition, analysis and data management, by following this link (https://teams.microsoft.com/l/team/19%3A85HZ7mBzO9MkHfY5T3Ns1qK1KTQC0-skSL1tQDEg6K81%40thread.tacv2/conversations?groupId=f70a1c00-51cd-4607-97ed-52b548ba3821&tenantId=09839d39-20e6-405d-8c08-dbc5e1ab3b3b).

Welcome to the Bioimaging Platform!

Dear (name of user),

You have asked for access to the [Oeiras Site] Bioimaging Platform (name of workstation) workstation. This workstation can be found in the Bartolomeu Dias wing (floor 0 of the main building).

Before giving you access to the workstation, here is some information about the Bioimaging computers:

• To use one of our workstations, you must book in Agendo, and sign out of your session once done with your analysis. If you intend to do analysis overnight, book the workstation until the next day, where you will be able to finish your analysis.

• All Bioimaging workstations have scripts to erase any data that has not been modified for more than 3 months (Imaris data processing drive is 1 month), meaning that you can work on old data, it just needs to actively be analysed.

• Even though the script exists, space is limited. Please transfer and erase all data from the workstations once you are done with your analysis, as the workstation has limited storage capacity (usually 8Tb), and many users with large datasets.

• Some workstations have Data Storage drives and Data Processing drives. The Data Processing drives are to be used solely for analysis, and never for data storage. They are faster, but very small in capacity (usually 2Tb). Always make sure you leave this drive as empty as possible once your session is done. You can either transfer the data back to the Data Storage drive, or the server.

• Most workstations have no backups, meaning that if the drive dies, your data is lost. Plan in advance, and backup all data to the server.

• If you require remote access to the workstations, that can be provided, just reply to this email, or send an email to bioimaging@gimm.pt.

Attention: The Bioimaging Platform is not responsible for unsaved work left after your booking is over.

Dear (name of user),

You have asked for access to the [Oeiras Site] Bioimaging Platform (name of workstation) workstation. This workstation can be found in the Bartolomeu Dias wing (floor 0 of the main building).

Before giving you access to the workstation, here is some information about the Bioimaging computers:

• To use one of our workstations, you must book in Agendo, and sign out of your session once done with your analysis. If you intend to do analysis overnight, book the workstation until the next day, where you will be able to finish your analysis.

• All Bioimaging workstations have scripts to erase any data that has not been modified for more than 3 months (Imaris data processing drive is 1 month), meaning that you can work on old data, it just needs to actively be analysed.

• Even though the script exists, space is limited. Please transfer and erase all data from the workstations once you are done with your analysis, as the workstation has limited storage capacity (usually 8Tb), and many users with large datasets.

• Some workstations have Data Storage drives and Data Processing drives. The Data Processing drives are to be used solely for analysis, and never for data storage. They are faster, but very small in capacity (usually 2Tb). Always make sure you leave this drive as empty as possible once your session is done. You can either transfer the data back to the Data Storage drive, or the server.

• Most workstations have no backups, meaning that if the drive dies, your data is lost. Plan in advance, and backup all data to the server.

• If you require remote access to the workstations, that can be provided, just reply to this email, or send an email to bioimaging@gimm.pt.

Attention: The Bioimaging Platform is not responsible for unsaved work left after your booking is over.