Release Note V4

LemnaLauncher V4.0.0 Changes of the new Release Improved performance for Scanalyzer Discovery plattforms

First issued: 25th April 2013 ŠLemnaTec 2013

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Raw Images Change Overview Before LemnaLauncher 4.0.0, all image data was stored as PNG files. After an image was acquired by the sensor, it had to be processed to that storage format. The processing is sophisticated if you want to get the most out of the image and can take a considerable amount of time. Depending on image size and speed of the control machine, the conversion could take a few seconds – per image, slowing down image acquisition and consequent throughput.

Beginning with LemnaLauncher 4.0.0, the image data is stored as raw binary data, exactly as received from the sensor. A content agnostic compression scheme is applied to the data to save storage space. The compression takes only a fraction of a second, even for large images.

Benefits Transforming image data from an arbitrary raw format to PNG is not only a time consuming task, but comes with the limitations of PNG as well (e.g. three channels, eight bits per channel only). That’s suffi1

PNG being a compressed

image

format

cient for colour images (like VIS or fluorescence), but in case of monochromatic data (NIR or height scan),

greatly

two of three colour channels of PNG are basically unused 1. NIR and height scan data have a higher resolu-

reduces the impact com-

tion than eight bits, which means that some information is lost in the process of PNG conversion (NIR

pared to an uncompressed

images) or the data is artificially transformed in a false colour format (height data). False colour images

image format, though.

make the actual image processing more complicated as the false colour conversion has to be inverted before the actual height scan data can be used.

Using unprocessed raw data, both of these points are addressed: no information is lost, because no conversion is needed. Image processing within the LemnaGrid can be done in arbitrary colour depths by utilising floating point data representation. The visualization of the raw data is done one the fly, allowing the selection of the most appropriate visualization technique. For example, height scan data can be visualized either as grey scale image, the classic false colour image or relief with level curves.

Postponing the image processing until all data is recorded and stored in the database brings another important benefit: different image processing methods can be used for different problems. While the standard Patterned Pixel Grouping algorithm for raw conversion is sufficient in most cases, the new Adaptive Homogeneity-Directed-Demosaicing method can capture critical details in some situations. The decision which conversion algorithm to use doesn’t need to be made until the experiment is done, giving researchers the chance to test different methods and to see which one shows the highest details and best results.

2

At least in a way that

resembles

the

Taking the raw image processing from recording time to analysing time requires the time saved when

original

recording has to be spent for each analysis performed. Processing time might be considerably longer if

image and is nice to look at

complicated raw conversion algorithms are employed. This can be mitigated by increasing the number of LemnaGridDaemons.

As computer screens show colour images, raw image data technically cannot be displayed2. Consequentially, the raw data has to be processed before it can be displayed at all. The LemnaLauncher utilizes a special, very fast conversion method to reduce the delay to the absolute minimum necessary.

3

File format description is

When image data is exported, it’s exported exactly the as it’s stored in the database. The images are

available from LemnaTec

written to RAWX-files3.

t

Lemnatec

LemnaTec GmbH · Schumanstr. 18 · 52146 Würselen · Germany Phone: +49 24 05 41 26-15 · info@lemnatec.com

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Move Images Overview Before LemnaLauncher 4.0.0, existed a parameter that sets the camera in the motion detection mode. A sequence of images is captured and then the camera performs the motion detection based on the parameters set beforehand. The motion detection transforms the sequence of images to a single image containing information about object motion in the sequence. This image is then stored in the database.

Beginning with LemnaLauncher 4.0.0, the motion detection is removed from the camera. Instead, parameters are added to the configuration to determine whether a sequence should be captured or a single image. The number of images in the sequence can be defined per configuration as well as the delay between two images. Both of these had to be fixed in the camera in older versions. The camera captures the whole sequence and stores the sequence in the database. The motion algorithm is applied in LemnaGrid.

Benefit Delaying the motion detection has several advantages: firstly, the way the new configuration works, parameters for the capturing of the sequence can be adjusted individually per configuration, which means different experiments on the same machine can use totally different sequence parameters.

Secondly, the actual motion detection is configured when the real data from the experiment is available.

One has the possibility to play around with varying motion detection algorithms and parameters without the need to recapture the images. Also, because the whole sequence is stored, the user can decide not to use the sequence at all. That’s not possible if only the processed image has been stored.

The third advantage is speed. Depending on the configuration, the motion detection can take a considerable amount of time. If this can be done later on instead of on the fly while capturing images, machine runtimes will be shorter. Although the new approach using a sequence of images in place of a single preprocessed image has several benefits, some things have to be kept in mind. As with raw images, moving image processing from capturing to the LemnaGrid means more time needed for analysis.

Additionally, storing a sequence of images instead of a single one takes up a lot more storage space, especially considering that the pre-processed images have quite compression friendly content. Much storage space per sequence can lead to longer machine running times, actually.

Offline mode Overview When starting the LemnaLauncher and initializing the machine every component is checked to ensure everything’s in working order. This includes database connections, as they the database is an integral part of the system.

During setup of the system, a configuration can be chosen that utilizes a cache for the database directly on the control computer. This cache acts as intermediate storage for images taken while the database is unreachable. Starting with LemnaLauncher 4.0.0 the LemnaLauncher can start and initialize even if the

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Lemnatec

LemnaTec GmbH · Schumanstr. 18 · 52146 Würselen · Germany Phone: +49 24 05 41 26-15 · info@lemnatec.com

database is not available (though images cannot be accessed as they haven’t been cached).

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Benefit The machine remains functional when database problems occur. Plants can be imaged and watered independent from the database. When database connection is re-established, all new images will be transferred.

Minor changes Turning velocity (Scanalyzer 3D Models) Fixed an error where sometimes an incorrect turning velocity is selected when IUCs with different turning velocities are combined.

Hide IUCs (DB) When configuring new databases, only IUCs that are available for inclusion in a new OAC can be copied (ensuring the copied IUC is available for use in the new database)

Tolerant system jobs (Scanalyzer 3 D Models3 r d generation variants only) Error-fix where sometimes the system jobs refused to start within the specified tolerance time although the system had the vacancies to start the system jobs. This only applies to the new 3 rd generation Scanalyzer3D.

t

Lemnatec

LemnaTec GmbH · Schumanstr. 18 · 52146 Würselen · Germany Phone: +49 24 05 41 26-15 · info@lemnatec.com