Image aquisition

Single snapshot images

To take images you should follow these steps:

• Make sure you have all the parts connected (camera cable, led control cable, HDMI cable to a screen, and power supply inputs)
• Turn on the raspberry pi
• Put the sample over the transilluminator
• Turn the LEDs on (digitally with python turnOn.py)
• Start the camera preview (type on the command-prompt: raspistill -t 0)
• Set the desired height of the camera with the knob (loosen a bit the knob -> move the camera → tighten the knob)
• Set the focus with the camera wheel
• Stop the preview with ctrl+c

In this way you can try different camera settings until you are happy (e.g. raspistill -t 0 -awbg 1,1 -ISO 200 -ss 50000). See camera settings for full documentation.

To save images to file include the -o option (e.g. raspistill -o image_name.tif)

Timelapse

• Make sure you have installed/updated the [camera python library][python library]
• Find proper camera settings following the previous procedure. It’s recommended to perform this task with a calibration sample (e.g. a previously grown plate with colonies of the strain of interest). You should provide fixed values for the ISO, the white balance (-awbg) and the exposure time (-ss) to have consistency in the data.
• Open timelapse.py and type the defined parameter values in the proper spaces and save the changes.
• Create a folder to store the images
• Execute the timelapse script python timelapse.py <folder name> <img filename prefix> <time step> <number of steps>

Move images

• You can get the images using a USB storage device, but it is not recommended to connect and disconnect devices on the Raspberry Pi USB ports meanwhile you are running a timelapse (it can generate undesired movement on your experiment).

• To remote/inline data transfer it is possible to move the files through a wifi connection by establishing a ssh connection or using software such as team viewer