Ivan Rey

Learning by watching: Explorations at the cellular scale and beyond
 


 (Aprendiendo al observar: Exploraciones en la escala celular y mas alla)


 Last week the inaugural version of Clubes de Ciencia Colombia event took place in Bogota and Medellin. The idea behind this program is to bring graduate students in the US back to Colombia to teach an intensive 1-week course (on a topic of their expertise) to kids finishing high school or starting college (see link: http://www.clubesdeciencia.co )


 I designed a microscopy course on which students could get a grasp on the theoretical and practical concepts behind microscopy. Professor Manu Forero at Universidad de los Andes and me were the instructors of the 15 kids (ages 14-17) that participated in the microword explorations course!


 
 Professor Manu Prakash very generously donated several Foldscope kits for this purpose.
 


 The main idea of the course was to teach the kids to assemble the foldscope, learn to use it, and then to learn to extract information of the images obtained. A secondary purpose was to teach them the multiscalar role of shape and structure in the biological function.


 Another objective of the course was to show the interdisciplinary nature of microscopy, from the physics required to understand the nature of light and optics laws, passing by the engineering involved in the actual assembly and operation of a microscope to the observations made thanks to microscopy that allow a better understanding of living beings and enrich biology.


 This course was sponsored by the Ondas program of Colciencias and Sena (governmental institutions) and it was held at Universidad de Los Andes in Bogota, Colombia.


 Below the schedule of the course per day as was actually given:


 
 Day 1:
 


 Instructors introduced themselves and explained how they got there (academic career)


 Lecture on the properties of light, light-matter interaction, Snell’s law (with practical demonstration) and lenses.


 The students visited the Biophysics lab at Uniandes and watched the optical setup of a light sheet microscope (SPIM), learned about fluorescence with samples and lasers, and observed by themselves Jurkat cells immunofluorescently labeled on an epi-fluorescence wide field microscope.


 
 Day 2:
 


 Students listened to Manu’s letter introducing them to the global network of microcosmos explorers (in Spanish of course)


 <a alt="2015-10-06-09.10.49.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-06-09.10.49.jpg">
 <img alt="2015-10-06 09.10.49" class="size-medium wp-image-9389 aligncenter gcloudimg" data-attachment-id="9389" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444122649","copyright":"","focal_length":"4.15","iso":"40","shutter_speed":"0.025","title":"","orientation":"1"}' data-image-title="2015-10-06 09.10.49" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-06-09.10.49.jpg" width="225"/>
 </a>


 The students assembled the Foldscope, learn to prepare and observe samples with the paper slides and used CR2032 batteries and LEDs to attach a light source to the microscope. The implementation of a dark field mode (using an acetate) was left as homework


 Lecture on the history of microscopy, focused on Van Leeuwenhoek microscope and observations.


 <a alt="2015-10-06-09.44.15.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-06-09.44.15.jpg">
 <img alt="2015-10-06 09.44.15" class="size-medium wp-image-9386 aligncenter gcloudimg" data-attachment-id="9386" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444124655","copyright":"","focal_length":"4.15","iso":"40","shutter_speed":"0.025","title":"","orientation":"1"}' data-image-title="2015-10-06 09.44.15" data-recalc-dims="1" height="225" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-06-09.44.15.jpg" width="300"/>
 </a>


 
 Day 3:
 


 Lecture on cell biology focused on the importance of the structure of the proteins and molecules in the formation of higher structures (Amphipathic lipids form membranes, polarized cytoskeletal proteins form the cytoskeleton) The concepts of thermal energy and the central dogma of biology were also introduced.


 The students were trained on the use of Fiji (ImageJ) to perform simple tasks like measuring the size of a cell or counting the number of protein clusters within a cell. The sample images used to teach were from immune cells that I use in my research and were taken with a variety of techniques that were briefly described to the students (TIRF, SMI, PALM, iSIM).


 <a alt="2015-10-07-13.38.37.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-07-13.38.37.jpg">
 <img alt="2015-10-07 13.38.37" class="size-medium wp-image-9387 aligncenter gcloudimg" data-attachment-id="9387" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444225117","copyright":"","focal_length":"4.15","iso":"40","shutter_speed":"0.025","title":"","orientation":"1"}' data-image-title="2015-10-07 13.38.37" data-recalc-dims="1" height="225" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-07-13.38.37.jpg" width="300"/>
 </a>


 
 Day 4:
 


 The students worked in small groups in the preparation of samples, capturing images with cell phones attached to the Foldscope, camera calibration and basic image analysis. The image below shows students measuring a bug using Fiji.


 <a alt="2015-10-08-11.21.45.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-08-11.21.45.jpg">
 <img alt="2015-10-08 11.21.45" class="size-medium wp-image-9388 aligncenter gcloudimg" data-attachment-id="9388" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444303305","copyright":"","focal_length":"4.15","iso":"40","shutter_speed":"0.025","title":"","orientation":"1"}' data-image-title="2015-10-08 11.21.45" data-recalc-dims="1" height="225" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-08-11.21.45.jpg" width="300"/>
 </a>


 The students were guided in the creation of an account at
 <a alt="www.microcosmos.foldscope.com" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/www.microcosmos.foldscope.com">
 www.microcosmos.foldscope.com
 </a>
 using their sticker number. Then all of them were requested to upload their observations including a description.


 Please see below the links corresponding to their posts:

<blockquote class="wp-embedded-content" data-secret="fZlKwg3UGg">
 
 <a href="https://microcosmos.foldscope.com/?p=9242">
 watching close a beauty flower – Viendo de cerca una bella flor
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="fZlKwg3UGg" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9242&amp;embed=true#?secret=fZlKwg3UGg" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="X3aMyr1YCw">
 
 <a href="https://microcosmos.foldscope.com/?p=9270">
 importancia de la sangre humana
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="X3aMyr1YCw" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9270&amp;embed=true#?secret=X3aMyr1YCw" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="1eoWRbEFWf">
 
 <a href="https://microcosmos.foldscope.com/?p=9267">
 muestra de sangre de un zancudo
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="1eoWRbEFWf" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9267&amp;embed=true#?secret=1eoWRbEFWf" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="Ae0DQq0rFC">
 
 <a href="https://microcosmos.foldscope.com/?p=9231">
 Comparación De Alas De Insectos Voladores
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="Ae0DQq0rFC" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9231&amp;embed=true#?secret=Ae0DQq0rFC" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="KNCCdDm7oQ">
 
 <a href="https://microcosmos.foldscope.com/?p=9213">
 Mandibula De Araña
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="KNCCdDm7oQ" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9213&amp;embed=true#?secret=KNCCdDm7oQ" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="mPqZSWuvgV">
 
 <a href="https://microcosmos.foldscope.com/?p=9209">
 Ojo De Araña
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="mPqZSWuvgV" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9209&amp;embed=true#?secret=mPqZSWuvgV" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="l499AUei5G">
 
 <a href="https://microcosmos.foldscope.com/?p=9201">
 bicho de agua sucia
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="l499AUei5G" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9201&amp;embed=true#?secret=l499AUei5G" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="QFub4yKhxg">
 
 <a href="https://microcosmos.foldscope.com/?p=9185">
 “Garra” Del Saltamontes
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="QFub4yKhxg" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9185&amp;embed=true#?secret=QFub4yKhxg" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="esQ27bJnUy">
 
 <a href="https://microcosmos.foldscope.com/?p=9142">
 la pulga de kira
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="esQ27bJnUy" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9142&amp;embed=true#?secret=esQ27bJnUy" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="eYHfoF1FGA">
 
 <a href="https://microcosmos.foldscope.com/?p=9137">
 POLEN
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="eYHfoF1FGA" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9137&amp;embed=true#?secret=eYHfoF1FGA" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="K1YoT06c0v">
 
 <a href="https://microcosmos.foldscope.com/?p=9125">
 Ala De Saltamontes
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="K1YoT06c0v" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9125&amp;embed=true#?secret=K1YoT06c0v" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="M4UhiEgf7j">
 
 <a href="https://microcosmos.foldscope.com/?p=9118">
 Fibras de tela sintetica roja – Red fibers of synthetic fabric
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="M4UhiEgf7j" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9118&amp;embed=true#?secret=M4UhiEgf7j" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="QFCAyXUoEe">
 
 <a href="https://microcosmos.foldscope.com/?p=9105">
 Estudio De La Forma Comprimida De La Sal
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="QFCAyXUoEe" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9105&amp;embed=true#?secret=QFCAyXUoEe" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>

<blockquote class="wp-embedded-content" data-secret="QFCAyXUoEe">
 
 <a href="https://microcosmos.foldscope.com/?p=9105">
 Estudio De La Forma Comprimida De La Sal
 </a>
 
</blockquote>

 <iframe class="wp-embedded-content" data-secret="QFCAyXUoEe" frameborder="0" height="338" marginheight="0" marginwidth="0" sandbox="allow-scripts" scrolling="no" security="restricted" src="https://microcosmos.foldscope.com/?p=9105&amp;embed=true#?secret=QFCAyXUoEe" style="display:none;" title="Embedded WordPress Post" width="600">
 </iframe>


 
 Day 5:
 


 The students finished their projects and worked in groups in the preparation of a poster (see final version) describing their work during the week.


 <a alt="Poster-MicromundoExploraciones2.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/Poster-MicromundoExploraciones2.jpg">
 <img alt="Poster-MicromundoExploraciones2" class="size-medium wp-image-9499 aligncenter gcloudimg" data-attachment-id="9499" 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="Poster-MicromundoExploraciones2" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/Poster-MicromundoExploraciones2.jpg" width="233"/>
 </a>






 Day 6:


 The students presented the poster to other kids (assisting to different courses), their parents and to grad students and university professors that assisted to the closing event.


 At the beginning they looked nervous (and very serious)


 <a alt="2015-10-10-10.27.23.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-10-10.27.23.jpg">
 <img alt="2015-10-10 10.27.23" class="size-medium wp-image-9390 aligncenter gcloudimg" data-attachment-id="9390" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444472843","copyright":"","focal_length":"4.15","iso":"40","shutter_speed":"0.016666666666667","title":"","orientation":"1"}' data-image-title="2015-10-10 10.27.23" data-recalc-dims="1" height="225" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-10-10.27.23.jpg" width="300"/>
 </a>


 They did a great job and many people was amazed by the Foldscope and on what this kids knew about microscopes and cell biology!


 <a alt="2015-10-10-10.19.25.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-10-10.19.25.jpg">
 <img alt="2015-10-10 10.19.25" class="size-medium wp-image-9391 aligncenter gcloudimg" data-attachment-id="9391" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444472365","copyright":"","focal_length":"4.15","iso":"32","shutter_speed":"0.025","title":"","orientation":"1"}' data-image-title="2015-10-10 10.19.25" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-10-10.19.25.jpg" width="225"/>
 </a>




 Dear Manu,


 This really was a life changing experience for this kids and for me! You provided a unique opportunity for this kids to learn about what surrounds them! The Foldscope was the perfect tool to introduce them into the wonders of the natural sciences and motivate them. Now several of them are interested in starting a career in science 🙂


 As for me, it was great to have the chance to bring back to Colombia the knowledge and experiences acquired studying abroad and realize the great potential of the colombian youth!


 Thanks a lot for your trust and for providing us with this amazing opportunity to grow!


 I’ll keep in touch!


 Ivan Rey


 <a alt="2015-10-09-12.55.25.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-09-12.55.25.jpg">
 <img alt="2015-10-09 12.55.25" class="size-medium wp-image-9394 aligncenter gcloudimg" data-attachment-id="9394" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444395325","copyright":"","focal_length":"4.15","iso":"32","shutter_speed":"0.00087719298245614","title":"","orientation":"1"}' data-image-title="2015-10-09 12.55.25" data-recalc-dims="1" height="225" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9385/2015-10-09-12.55.25.jpg" width="300"/>
 </a>

Learning by watching: Explorations at the cellular scale and beyond

Last weekend while I was preparing a microscopy course based on the use of the foldscope I started looking for samples at my parent’s house. In their garden they have a water fountain that is frequently visited by birds (birds usually take baths there and use them as restroom too) the water of this fountain looked really murky so I took a little and looked at it under the Foldscope (low mag lens), I was not disappointed!


 I found a very interesting bug of about 900 um in length


 <a alt="2015-10-04-19.35.32.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.35.32.jpg">
 <img alt="2015-10-04 19.35.32" class="size-medium wp-image-9399 aligncenter gcloudimg" data-attachment-id="9399" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1443987332","copyright":"","focal_length":"4.15","iso":"32","shutter_speed":"0.0059171597633136","title":"","orientation":"1"}' data-image-title="2015-10-04 19.35.32" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.35.32.jpg" width="225"/>
 </a>


 When I looked closer at it I found what looks like a paramecium! (On your left)


 <a alt="2015-10-04-19.35.51.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.35.51.jpg">
 <img alt="2015-10-04 19.35.51" class="size-medium wp-image-9400 aligncenter gcloudimg" data-attachment-id="9400" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1443987351","copyright":"","focal_length":"4.15","iso":"32","shutter_speed":"0.0059171597633136","title":"","orientation":"1"}' data-image-title="2015-10-04 19.35.51" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.35.51.jpg" width="225"/>
 </a>


 Zooming out I was able to observe that the bug was next to what looked like a dead mosquito larva (this image in particular was taken few days later)


 <a alt="2015-10-07-12.57.05.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-07-12.57.05.jpg">
 <img alt="2015-10-07 12.57.05" class="size-medium wp-image-9401 aligncenter gcloudimg" data-attachment-id="9401" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1444222625","copyright":"","focal_length":"4.15","iso":"100","shutter_speed":"0.033333333333333","title":"","orientation":"1"}' data-image-title="2015-10-07 12.57.05" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-07-12.57.05.jpg" width="225"/>
 </a>


 Then, by zooming in on the dead larva I found what looked like an scavenger carnival! Several unknown (for me at least!) life forms (any ideas on what are those?)


 <a alt="2015-10-04-19.38.21.jpg" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.38.21.jpg">
 <img alt="2015-10-04 19.38.21" class="size-medium wp-image-9402 aligncenter gcloudimg" data-attachment-id="9402" data-comments-opened="1" data-image-meta='{"aperture":"2.2","credit":"","camera":"iPhone 5s","caption":"","created_timestamp":"1443987501","copyright":"","focal_length":"4.15","iso":"32","shutter_speed":"0.0038022813688213","title":"","orientation":"1"}' data-image-title="2015-10-04 19.38.21" data-recalc-dims="1" height="300" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.38.21.jpg" width="225"/>
 </a>


 I was so excited that I even recorded a video and captured very small (unidentified) creatures moving around!


 <a alt="2015-10-04-19.37.22.mov" class="gcloudimg" href="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_9398/2015-10-04-19.37.22.mov">
 2015-10-04 19.37.22
 </a>

Ivan Rey

Earth

Posts

Learning by watching: Explorations at the cellular scale and beyond

In a drop of fountain water

Locations

Statistics

Type of Sample

Foldscope Lens Magnification