External Storage Devices
The Flamingo requires an external storage device for recording image data. During an experiment, the storage device is connected to the camera workstation’s USB port.
A Flamingo can generate a large amount of image data even during short experiments. Some examples of typical experiments and the generated data size is shown below. Keep in mind that you might want to reserve additional storage space to save processed images.
|Z-stack with 200 planes and 3 channels||5 GB|
|Multi-view recording with 6 angles, 200 planes and 3 channels||30 GB|
|12 hour time-lapse with 100 planes, 2 channels and 5 min interval||240 GB|
|2 day time-lapse with 2 positions, 150 planes, 2 channels and 10 min interval||1.5 TB|
|2 hour continuous recording with 25 ms exposure time||2.5 TB|
The storage device needs to fulfill the following requirements:
- USB connectivity, ideally USB 3.1 Gen 1 or 2, with a USB-A type connector for the camera workstation
- > 350 MB/s write speed for uninterrupted recording at full camera speed*
- > 1 TB storage space**
*) Considering a PCO Panda running at 40 fps with 2048×2048 pixels (8.4 MB/image). Slower devices can be used, but might impose additional latency during experiments. Faster devices have additional benefits for post processing right on the device.
**) Required storage space depends on user requirements. The Flamingo records 8.4 MB images. This number needs to be multiplied by the number of channels, planes, positions, views and timepoints.
We recommend using solid state drives (SSDs), either homebuilt combinations of internal SSDs in USB enclosures or pre-configured external SSDs. Specific products that we tested are listed below.
We do not recommend recording images to hard disk drives (HDDs) because of the high risk of drive failure and data loss. To achieve the required write speed, several HDDs need to be combined in a fast RAID configuration (typically RAID-0 without redundancy), further increasing the risk of failure.
2 TB Intel 660p in Plugable USB-C enclosure
A large SSD in an external USB enclosure is a good choice as external storage device for the Flamingo. The Plugable USB-C Enclosure supports M.2 NVMe SSDs and USB 3.1 Gen 2. A matching SSD is the Intel 660p 2TB. Compared to other solutions, this combination is affordable and very fast.
- 2 TB storage
- 900 MB/s write
- 900 MB/s read
2x 4 TB Samsung QVO/EVO in Mediasonic ProRaid USB-C enclosure
An external RAID enclosure such as the Mediasonic ProRaid USB-C with two of the Samsung 860 EVO SSD 4 TB or the slightly cheaper Samsung 860 QVO SSD 4 TB configured as RAID-0 provides plenty of space and high write and read speeds in a compact package.
- 8 TB storage
- 820 MB/s write (2x Samsung QVO)
- 860 MB/s read (2x Samsung QVO)
8 TB Micron ION in ICY BOX USB-C enclosure
4 TB Samsung QVO/EVO in Ugreen USB-C enclosure
2 TB Sandisk Extreme Portable SSD
The SanDisk Extreme Portable SSD 2 TB is an all-in-one solution.
- 2 TB storage
- 470 MB/s write
- 500 MB/s read
512 GB Patriot Supersonic Rage 2 USB Stick
The Patriot Supersonic Rage 2 512 GB USB stick did not achieve our recommended write speed and does not have a large storage capacity, but can be a handy option for test runs and less demanding experiments.
- 512 GB storage
- 150 MB/s write
- 350 MB/s read
Write and read speeds are measured with the drives connected via USB-C to an Apple MacBook Pro 2018 running macOS 10.14.5/6 and the Blackmagic Disk Speed Test.
Working with recorded images
Loading individual Files
The Flamingo saves recorded image data as raw files, a fast and efficient format. Each stack is saved as a single file. Individual raw files can be imported into Fiji via File > Import > Raw… or by drag-and-drop. Adjust the following settings during import:
- Image type: 16-bit Unsigned
- Width & Height: 2048 (unless cropped)
- Number of images: ≥ number of planes
- Little-endian byte order
Converting a large number of files
Once you have a large number of image files in a given experiment folder, an automated conversion and pre-processing is desirable. These two Fiji tool converts image files recorded with a Flamingo microscope into tif files. Options for max projection, small preview, cropping and combining two illumination sides are present. Files are saved to subfolders.
FlamingoConverter.ijm is designed for the latest iteration of Flamingo microscopes. It is compatible with both raw and tif output.
Flamingo_RAWtoTIF.ijm was written for the previous iteration of Flamingo microscopes, which only had raw output.