CODI-FAQ
What is CODI ?
Our CODI cloud platform is a beta and is currently an analysis platform used for the analysis of data acquired by our Nanoimager and its local acquisition software (NimOS).
CODI is...
- A collaborative platform to share your data and analyses with colleagues and the public, opening up new possibilities for cross dataset insights and allows us to benefit from the expertise of our peers beyond the walls of our institution.
- A unique cloud-based platform that allows users to easily acquire, organize, visualize and analyze data from everywhere, using a laptop or a phone.
- A quantitative analysis platform specifically designed to work with single-molecule localization data and uses advanced algorithms to provide quantitative information from users’ localization-based super resolution experiments.
Who can use CODI?
CODI is currently a beta version, and not publicly available yet. Only our customers in possession of the CODI URL are able to register and access the CODI cloud platform.
To sign up for CODI, users need minimal personal information collected for authentication to the CODI platform: name and email address. It is also possible to authenticate through Google.
CODI is a platform developed for the analysis of data acquired by our microscope and its local acquisition software (NimOS). Users can upload their dataset to the platform for organization, visualization and analysis purposes (What type of datasets can I analyze on CODI?). Internet access is required to be able to use the platform (What kind of computer power, internet connection do I need?).
How to delete datasets, collaborations and accounts on CODI ?
Scientific insights are held back by barriers to data-sharing and collaboration. ONI’s mission is to remove these barriers to discovery and maximize the impact from every experiment. CODI provides a conducive environment for sharing and collaboration.
You can delete a collaboration if it is empty. However, as a user, you cannot delete the datasets and user account on CODI, but you have other ways to achieve this:
- You will be able to archive your datasets and decide to display those or not from your account (feature coming soon).
- You can use collaboration or tag features to filter your datasets among your data uploaded to the cloud and clean your space.
- You can always contact the customer support to delete datasets and user accounts from the cloud platform for privacy and confidentiality questions. Note that this type of action remained for now case by case.
What type of datasets can I analyze on CODI?
CODI is specifically designed to work with single-molecule localization data and uses advanced algorithms to provide quantitative information. For now, CODI provides the ability to analyze only multi-color localization data.
Note that live cell imaging and single particle tracking analysis is not supported. In the future, the platform will allow for the visualization and analysis of different imaging modalities.
Upload and download datasets into CODI
Dataset files can be imported or exported from CODI cloud platform. As a beta version, there is currently no limitation per user account for data cloud storage and upload (see Data storage limitation section).
You can import NimOS acquisition files using the upload feature in CODI (see screenshot below). To upload a dataset in CODI several files are required: .locb (or .pointcloud), _map.nim, _acq.nim, and any files with the same prefix can be added. Once added and cloud optimized, the uploaded datasets are stored on your user account space. Note that if they can be uploaded, CODI is not able to process any raw data for now.
The Desktop Uploader is a feature that is coming soon. This is a new local application that has been developed to automatically upload your local files into the cloud more easily and in an intuitive way (How to guide: The CODI Desktop-Uploader).
From the dataset information page, you can export the individual files which will be saved locally. However, we don’t recommend to use CODI to manage raw data, as the upload process will take longer time and slow down your experience on the platform. Note that from the same feature panel, you can also add more files to the dataset.
How to export data results and graphs?
On CODI, you can analyze your point-cloud data and extract parameters and quantitative features via the different analysis tools.
You can export/import the analysis parameters used for each CODI analysis tool (see picture below). You can export localization filters, temporal groups filters, cluster constraints and counting filters. The parameters are exported in .json files.
You can export graphs and histograms as .png or .svg files via the different analysis tools.
You have the possibility to export quantitative results from the clustering, counting tool as well as extracting a summary report.
From the clustering tool:
- Go the clustering tool
- Run the clustering algorithm and apply constraints if needed.
- Go the the back menu of the clustering tool
- Download the clustering results table in .csv file format
From the counting tool:
- Go the counting tool
- Run the counting algorithm
- Defined your settings and set positivity threshold(s)
- On the scatterplot settings, download the positivity table in .csv format
- Below the counting tool, download the summary report combining clustering and positivity results
CODI License agreement and GDPR compliance
At ONI, we are working on official documentation (GDPR compliance) that will be available within the year. Public datasets on CODI are published under the Creative Commons Attribution-ShareAlike 4.0 license. CODI, including its design, source code, analysis tools, and other associated material is protected under Copyright.
CODI is a cloud platform using a secure database hosted with Google Cloud Platform (located in Belgium).
Users can upload their dataset to the platform for organization, visualization and analysis purposes. Internet access is required to be able to use the platform. Data can be uploaded as public, Private or Shared (Private by default). Private data cannot be viewed by anyone it is not shared with through the platform.
Users who sign up to CODI are only required to provide the minimal amount of personal information: name and email address, collected for authentication to the CODI platform. It is also possible to authenticate through Google, in which case we source the data from the user’s Google account. No personal data is transferred to third parties.
How to access Tutorial on CODI ?
Follow our step by step tutorial mode to guide you through our new CODI feature. To launch the different tutorials, go on the “help” menu and click on the “car” icon, select your tutorial and the tour should start (see .gif below). Note that for now, only the collaboration tour is available, but more features and tutorials are coming !
How to organize your data in CODI ?
Organization
Using our tool “Collaborations'' you will be able to organize, share and structure your super-resolution data inside CODI. (How to guide: How to share and organize your data). Single tags or key-value tags can be applied to every dataset uploaded onto CODI. Using tags, you will be able to organize your data within your personal or shared dataset or more specifically inside your Collaborations.
Sharing
On CODI, uploaded datasets can be defined as Private, Public or Shared. By default, uploaded datasets are set private, and private datasets cannot be viewed or analyzed by anyone it is not “shared” with through the platform. Users have access to other user datasets only if they are public or shared specifically with them. Public datasets are available to anyone owning a CODI user account and exposed in the main gallery. Public datasets give the opportunity to users from the world to access its visualization and analysis.
Sharing dataset on CODI, gives different levels of permissions: Viewer, Analyst and Owner (Dataset Sharing and Permissions).
Upload and download
You can import and export datasets on CODI easily via different tools (Upload and download datasets into CODI).
Dataset Sharing and Permissions
Sharing dataset on CODI, gives different levels of permissions: Viewer, Analyst and Owner. Permissions are decided at the Collaboration and dataset level. On schemas below, you can find a resume of actions allowed or not depending on the ownership type at Datasets or Collaborations level.
It is not possible to revoke permissions for a single dataset if they are granted by the Collaboration without removing the dataset from the Collaboration. All datasets added to a Collaboration have at least the permissions associated with the Collaboration but the owners of the dataset or Collaboration may add further permissions. (i.e., you can share a dataset to someone who does not have Collaboration permissions).
Data storage limitation
There is currently no limitation on the size of data uploaded and the amount of data stored per user account. Note that users don’t have to upload the raw .tiff images to be able to visualize and analyze their point-cloud data on CODI.
How to report a bug, request features and submit a question ?
You can report a bug and request features from the CODI platform directly. From the help menu, i.e the “question mark” button at the bottom-left hand corner of CODI, you can access the CODI help-center to submit and request your bugs and features (see screenshot below).
How to register for the CODI service desk?
To register for the CODI service desk, all that is required is your name and email address. Once you sign-up, a member of Customer Success team will verify your account.
The CODI service desk provides how-to-guides which are updated with new articles when new features are released. Additionally, if you are having any issues with CODI or require any support from the CX team, you can submit a ticket on our CODI service desk and a member of the CX team will assist you.
Which browser to use for CODI ?
Any browser can support CODI, however we recommend the use of chromium-based browsers (e.g. Chrome, Edge, Brave, Opera, etc.) which have shown more reliability for regular usage.
What kind of computer power, internet connection do I need?
No particular local resources are needed, however, we advise our customers to launch CODI on a modern device which we recommend has a minimum 8GB of RAM. In order to use CODI, your device requires internet access. Any broadband connection should be acceptable but we recommend a minimum of 12Mbps and 24Mbps for the upload of large datasets.
Which devices (phone, ipad, laptop) are supported by CODI?
Every kind of support with an internet access can be used for CODI: laptop, phone, tablet, etc.
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