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picroscopy's Introduction

picroscopy

Picroscopy is a small Python web-application which is intended for usage with a Raspberry Pi as a microscopy solution. With the Raspberry Pi Camera mounted on a microscope, the Raspberry Pi provides a live video feed to its monitor via HDMI, while another machine can be used to control the setup via a web-based interface.

The project is written in Python 3 and is open-sourced under the GPL license. Packages can be downloaded from the project homepage. The source code can be obtained from GitHub. The documentation can be read on ReadTheDocs.

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picroscopy's Issues

Add image format selection

Should have the ability to use a lossless output like PNG. Scientists will almost certainly want TIFF output too. One question is how to preserve Exif data with these other formats (ought to be possible with TIFF given that's where Exif originated - no idea about PNG and whether PIL/Pillow supports writing Exif at all, let alone to non-JPEG formats).

RPi system settings

Permit user to configure DHCP/static addressing, DNS servers, hostname (does this affect DHCP client ID?), and client IP lock (still need to add the latter).

Remove reliance on external binaries

If possible, attempt to interface to the camera directly with MMAL. If this is successful, attempt to incorporate image overlays (OpenGL/ES?)

Check out embedded thumbnails

Now we can configure thumbnail settings in picamera, it might be worth seeing if we can extract the embedded thumbnail from JPEGs and use it instead of a separate thumbs directory?

RPi startup script

Need a wrapper script which will start picroscopy on boot and, depending on exit code, shutdown or reboot the RPi, or possibly upgrade picroscopy (if possible?)

Display server IP

Assuming new installation will be using DHCP and that the RPi will have no (proper) DNS name. Display IP address prominently on startup (image? ASCII art?).

Side issue: what if RPi is using wlan0 instead of eth0? Should we support this?

Add JPEG quality setting

Users should have the ability to specify the level of compression of the JPEGs. There should probably be some warning for silly settings like <75 or >95.

Scale bars

Check out how to draw scale bars on generated images then provide the following settings:

  • Scale bar enabled/disabled
  • Scale bar position (top-left, bottom-right, etc.)
  • Selected lens

In the configuration file, use a separate section to dictate the available lenses and the scale of their scale bars, when active

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