Of Baby Trees Chocolate Mountain

<figure class="wp-block-image">
 <img alt="20190507_161540_scale" class="wp-image-148225 gcloudimg" data-attachment-id="148225" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="20190507_161540_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148223/20190507_161540_scale.jpg"/>
 <figcaption>
 Shrimp abdomen sample
 </figcaption>
</figure>
<figure class="wp-block-image">
 <img alt="20190507_171926_scale" class="wp-image-148226 gcloudimg" data-attachment-id="148226" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="20190507_171926_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148223/20190507_171926_scale.jpg"/>
 <figcaption>
 Shrimp tail sample
 </figcaption>
</figure>

 We took samples of small sundried shrimps of the were put in a slide and observed with the foldscope. The two images shown views of samples from the abdomen and the Lateral ramus part of the tail. We  observe how the samples from the abdomen are mostly translucent and most the back illumination for the LED lamp pass through and give a “crystal” effect. On the samples with the tail we observe what appear to be longitudinal fiber that provide strength to the tail and the irregular endings characteristics of crustacean tails. We have included a scale bar depicting 100 um that was obtained by taking a photo with the foldscope of 2 orthogonal 1 mm lines with the same elevation as the sample photo and dividing the length into 10. The scale bars were inserted into the image using Matlab.

Shrimp abdomen and tail samples

In the spirit of reproducibility, our group decided to get data from the local supermarket. For this post we will focus on the anchovies we obtained. The anchovies are the dehydrated ones found in packets, and they are usually added as flavoring to soups and other dishes.


 The first sample of the anchovy we examined using the foldscope was a cross section of the eye that contains the crystalline lens and aqueous humor. Here we observe the loss of structure of the sample, especially of the lens which can be seen as the dark spots near the top of the image, and the anchovy appears to have become discolored due to the dehydration and preservation process.

<figure class="wp-block-image">
 <img alt="fish_eye_scale" class="wp-image-148237 gcloudimg" data-attachment-id="148237" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="fish_eye_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148224/fish_eye_scale-1.jpg"/>
</figure>

 The inclusion of surrounding anchovy tissue in the sample makes it difficult to determine exactly which part of the eye is being shown, but the lens and aqueous humor are visible. The images were then post processed by adding a scale bar (100 um). This was done by imaging 1mm length lines using the foldscope and calibrating the images we took of the samples to the images with the 1mm lines. We then added the scale bars to the corner of the foldscope image using a matlab script. Contrast was additionally enhanced through post processing using a neural network. This was done to evaluate what we believe to be a bad example of post processing. As can be seen in the second contrast enhanced image, the style transfer based post processing may suffice as an art piece, but it does not add any meaningful improvements to the image.


 Below is the contrast enhanced image for the fish eye sample:

<figure class="wp-block-image">
 <img alt="fish_eye_post_scale" class="wp-image-148238 gcloudimg" data-attachment-id="148238" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="fish_eye_post_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148224/fish_eye_post_scale.jpg"/>
</figure>

 We then repeated this process for a sample taken from the anchovy gill flap. The image was acquired under the same conditions and with the same methodology for generating the scale bar. We also applied contrast enhancement through a style transfer neural network to provide an example of bad post processing.


 Below is the gill flap sample with scale bars:

<figure class="wp-block-image">
 <img alt="fish_gill_flap_scale" class="wp-image-148245 gcloudimg" data-attachment-id="148245" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="fish_gill_flap_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148224/fish_gill_flap_scale.jpg"/>
</figure>

 Below is the style transfer network post processed sample:

<figure class="wp-block-image">
 <img alt="fish_gill_flap_post_scale" class="wp-image-148246 gcloudimg" data-attachment-id="148246" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="fish_gill_flap_post_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148224/fish_gill_flap_post_scale.jpg"/>
</figure>

Dehydrated Anchovy Samples #BioE301C

Cnidarians are a phylum of principally marine invertebrates that includes
 
 inter alia
 
 coral, anemones, and jellyfish. A defining feature of a cnidarian is its
 
 nematocyst
 
 or
 
 cnidocyst
 
 , the secretory subcellular capsule responsible for delivering a cnidarian’s characteristic sting
 
 .
 
 The kinetics of nematocyst discharge can occur on the nanosecond scale, providing an acceleration upwards of 5 million g. Cnidarians generally have a radial body plan with a rudimentary nervous system. This nerve net does not exhibit cephalisation and is instead distributed.

<figure class="wp-block-image">
 <img alt="20190507_165437_scale" class="wp-image-148383 gcloudimg" data-attachment-id="148383" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="20190507_165437_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148380/20190507_165437_scale.jpg"/>
</figure>

 We obtained a sample of a scyphozoan, or true jellyfish, from a local supermarket and examined its microscopic structure. The sample was derived from the organism’s tentacle, the principal site of nematocyst concentration. The sample was translucent in character; the interior of the specimen is to the bottom and left of the provided images. Although some structure is evident, it’s not apparent whether this is due to the organism’s internal organization or a consequence of the dissection and preservation process.

<figure class="wp-block-image">
 <img alt="20190507_165043_scale" class="wp-image-148384 gcloudimg" data-attachment-id="148384" data-comments-opened="1" data-image-meta='{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}' data-image-title="20190507_165043_scale" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_148380/20190507_165043_scale.jpg"/>
 <figcaption>
 
 </figcaption>
</figure>

Of Baby Trees Chocolate Mountain

Earth

Posts

Shrimp abdomen and tail samples

Dehydrated Anchovy Samples #BioE301C

Unknown scyphozoan

Locations

Statistics

Type of Sample

Foldscope Lens Magnification