Ali Akib

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 <figcaption>
  105133-01-AK (green organisms)
 </figcaption>
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<p>
</p>
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 <img alt="20181217_134831" class="wp-image-105154 gcloudimg" data-attachment-id="105154" data-comments-opened="1" data-image-meta='{"aperture":"1.9","credit":"","camera":"SM-J700H","caption":"","created_timestamp":"1545054511","copyright":"","focal_length":"3.7","iso":"40","shutter_speed":"0.0026881720430108","title":"","orientation":"6"}' data-image-title="20181217_134831" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105133/20181217_134831.jpg"/>
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 <img alt="20181217_134751" class="wp-image-105155 gcloudimg" data-attachment-id="105155" data-comments-opened="1" data-image-meta='{"aperture":"1.9","credit":"","camera":"SM-J700H","caption":"","created_timestamp":"1545054471","copyright":"","focal_length":"3.7","iso":"40","shutter_speed":"0.0018083182640145","title":"","orientation":"6"}' data-image-title="20181217_134751" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105133/20181217_134751.jpg"/>
 <figcaption>
  105133-02-AK
 </figcaption>
</figure>
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 <img alt="20181217_181317" class="wp-image-105132 gcloudimg" data-attachment-id="105132" data-comments-opened="1" data-image-meta='{"aperture":"1.9","credit":"","camera":"SM-J700H","caption":"","created_timestamp":"1545070397","copyright":"","focal_length":"3.7","iso":"40","shutter_speed":"0.0029940119760479","title":"","orientation":"6"}' data-image-title="20181217_181317" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105133/20181217_181317-3.jpg"/>
 <figcaption>
  105133-03-AK
 </figcaption>
</figure>
<p>
</p>


What are these?

<p>
 My journey to the microscopic world began with an ordinary microscope about a year ago. I faced various problems while using it like some thing grew on the lens and blurred the view, it was heavy and not easy to carry and so on. So, I googled ‘Microscope problems’ and watched a video on foldscope by Manu Prakash on TED. I got amazed and immediately decided to buy one. At last I got it only two weeks ago . Many of my problems were solved. I also got the solutions regarding collection of planktons by making a plankton net (https://microcosmos.foldscope.com/?p=17431), making a portable reflection microscope (with foldscope) by a simple hack (https://microcosmos.foldscope.com/?p=33534), making a super cheap  centrifuge called ‘paperfuge’ (see http://web.stanford.edu/group/prakash-lab/cgi-bin/labsite/wp-content/uploads/2017/12/Paperfuge.pdf for the full PDF). But some problems are left.
</p>
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 <img alt="imagesGW4SV0QP" class="wp-image-105815 gcloudimg" data-attachment-id="105815" 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="imagesGW4SV0QP" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105762/imagesGW4SV0QP.jpg"/>
</figure>
<p>
 Your guess is right. It is the ‘Dye or Stain Problem’. Dyes/ stains have added a new dimension in microscopy. But dyes/stains for microscopic purposes are rare in many places. In most cases there is no shop where you can find them.
</p>
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 <img alt="images7MBVJ051" class="wp-image-105816 gcloudimg" data-attachment-id="105816" 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="images7MBVJ051" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105762/images7MBVJ051.jpg"/>
 <figcaption>
  Dyed Glomerulus viewed under microscope.
 </figcaption>
</figure>
<p>
 So, how can it be solved? The only answer is cooperation. If anyone who knows how to make dye out of cheap and available materials  help us by giving a nice post about making them, it would surely be solved. Anyone please make such a post so that we can have homemade cheap dyes.
</p>
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 <img alt="imagesOTBS646X" class="wp-image-105819 gcloudimg" data-attachment-id="105819" 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="imagesOTBS646X" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105762/imagesOTBS646X.jpg"/>
 <figcaption>
  A dyed WBC surrounded by RBCs.
 </figcaption>
</figure>
<p>
 There are many kinds of them. But only a few dyes would work. If you are to write such a post please tell us the process of using it (like how long the sample should be dipped inside the dye) and where it can be used (like some dyes only work for gram positive bacterias).
</p>
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 <img alt="imagesRHDEY1J3" class="wp-image-105836 gcloudimg" data-attachment-id="105836" 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="imagesRHDEY1J3" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105762/imagesRHDEY1J3.jpg"/>
 <figcaption>
  Gram positive (violet) and gram negative (pink) bacterias
 </figcaption>
</figure>
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 <img alt="imagesVQBBJCHK" class="wp-image-105818 gcloudimg" data-attachment-id="105818" 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="imagesVQBBJCHK" data-recalc-dims="1" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_105762/imagesVQBBJCHK.jpg"/>
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<p>
 <strong>
  An Additional Request:
 </strong>
</p>
<p>
 Please create a post for making a cheap microtome. This post is good (https://microcosmos.foldscope.com/?p=25948) but I need a better one for making it.
</p>
<p style="text-align:right">
 <em>
  Note: The pictures were taken from internet.
 </em>
</p>


A request

Old observations

<p>
 This post aims at changing microcosmos foldscope through it’s suggestions. I request the foldscope team to read the suggestions and foldscope community (especially learned ones) to check the questions part below:
</p>
<p>
 <strong>
  <em>
   Suggestion 01:
  </em>
 </strong>
</p>
<p>
 In microcosmos foldscope, there’s a huge collection of observations of a vast variety of organisms (especially microorganisms). So there’s a huge possibility of finding new species in this website. Some well educated ones the foldscope community are trying to identify them upto a certain taxonomic rank. But it’s not enough to discover new species or identify exactly upto species level in most cases. They try to identify as many organisms as they can and I highly appreciate it. However, it is not possible to identify all of them or even to notice all of them. For example most of the organisms in my previous post (
 <a href="https://microcosmos.foldscope.com/?p=108935">
  old observations
 </a>
 ) are still not identified. So, I suggest to introduce a new system that I call ‘Identification request’.
</p>
<p>
 In this system, the foldscopers (authors) will observe an organism and after taking video, pictures and information of it, they will publish a post on it following the general rule. But before publishing, there will be an option in the settings part of the post named ‘identification request’. If he/she wants to identify any organism in his/her post, he/she will click on it. Then, he/she has to choose certain blocks in his/her post that contains the video, picture, information etc of the organism he/she wants to identify. Lastly, he/she has to make a guess about the organism’s identity (in which kingdom/ phylum / class etc it belongs to) and its observation type (normal or phenomenon, physical or biological). It can be done in two ways. Either he/she can give the name of a certain taxonomic rank only or the whole chain of it upto which he/she can identify. He/she can also keep it blank. If the post has information of more than one organism which are needed to be identified , he/she will make multiple identification requests for each of them in the same post.
</p>
<p>
 For example, Mr. X have found a copepod and another organism he couldn’t identify. He can’t go any deeper in the taxonomic ranks of the copepod and the other organism. So, he makes two idenitfication requests. He names them as per the convension that @manu (along with @laks) made in the comments of the post ‘
 <a href="https://microcosmos.foldscope.com/?p=16599">
  A gift that keeps on giving – flowers from Mother’s Day
 </a>
 ‘. Then, he gives the identifications by either writing subclass copepoda only or writing kingdom animalia, phylum arthropoda, class maxillopoda, subclass copepoda, order unknown for the copepod. For the other organism, he names it as per the previous process and keeps the identification blank. The identification requests are done. They will go to a special inbox for identification requests.
</p>
<p>
 There wil be a group of selected people (by the foldscope team or the team itself) called ‘primary identifiers’. Only they can check the inbox. They will see the requests and correct any mistake that they find in it ( like the video has some problems, the group of selected blocks have two same looking but different organisms, the identification of the foldscoper was wrong, the request is fake etc). They will try to correct these by making comments or sending emails or any other way. Then the foldscoper will solve these by editing their identification request. If it is fake, the primary identifiers can discard it. Then, the primary identifier will do a quick identification try of the organism. He/she will not desperately  search for the genus or species of the organsim but will only identfy it upto which he/she can at first sight. Then he/she will place the organism’s observation in a file of a special database which represent his/her identification.
</p>
<p>
 The databse will be called ‘Foldscope Observation Database/FOD’ where identfication requests are placed in an orderly manner by dividing into taxonomic rank (kingdom, phylum, class …). It can be seen by anyone but can be edited by only two groups of people (primay and secondary identifiers which I will discuss later below). There will be both identification requests and observations of organisms which are already identified (if they are selected by the primary or secondary identifiers while searching microcosmos foldscope). It can also contain physical phenomenon or observations (like microfluidics, polarized microscopy of salts etc). The process of placing observations in there will be:
</p>
<p>
 First option will be whether it is physical or biological. In biological part, there will be files for each taxonomic level (like kingdom, phylum, class…). Like for kingdoms: Archaea, Bacteria, Protista, Chromista, Fungi, Plantae, Animalia, Unidentified. Phylum (Kingdom Animalia): Porifera, Cnidaria, Platyhelminthes…. Chordata, Unidentified. It goes on in this way. The primary identifier has to select every file in which the organism belongs to step by step. Primary identifiers can also make new files for new taxonomic ranks (like new genus/family/order etc).
</p>
<p>
 For example: in the case I described in the earlier example of Mr. X, Mr. Y (a primary identifier) saw the copepod and identified it to be of the genus
 <em>
  Diaptomus
 </em>
 . So he places the observation in FOD in the following way: Observation: Biological, Type: Total, Kingdom: Animalia, Phylum: Arthropoda, Subphylum: Crustacea, Class: Maxillopoda, Subclass: Copepoda, Order: Calanoida, Family: Diaptomidae, Genus:
 <em>
  Diaptomus
 </em>
 , Species: Unknown.
</p>
<p>
 **Note: Biological observations can be divided into three types: Total, Partial and Phenomena/event. In Total observations, full body of organisms (or at least most of it) is observed (like in case of microorganisms). In Partial observations, only a part of the organism is observed (like plant leaf cell observation). If all parts of the organism are present in the observation in different partial observations, it will be a Total observation. Like if an observation contains all parts of a plant (leaves, roots , stem, fruits, flowers etc) it will be a total observation. In case of Phenomenon observations, it will be a biological phenomenon that the foldscoper couldn’t understand. Like are these living or not? (seeing brownian motion of non living things).
</p>
<p>
 In case of physical observations, there will be three types: Dynamic, Non-dynamic and Material. Dynamic observations include motion (like microfluidics). Non dynamic observations include those that do not have any motion (like observing salt keeping a polarization filter). Material observations include observing materials by microscope for interesting patterns (like observing crystals and nanoparticles). Note that the Identification request can also be done for physical ones and in that case, one has to select the observation maintype Physical instead of maintype Biological while making the identification request.
</p>
<p>
 To finalize the identification request, the primary identifier will make a comment/send email/message to the foldscoper saying things like these: “Your identification request no. 13405 of 126000-05-NM organism (copepod) is accepted. It was identified upto genus level named
 <em>
  Diaptomus
 </em>
 . For more information, go to FOD and search request no. 13405. Wait for final identification”. He/she can include any extra information like this organism might be parasitic, this organism is used to make an extract/enzyme etc. If it is done on a daily basis (once a day) it should take 10-15 minutes at best to accept 20-30 requests per day.
</p>
<p>
 Now comes the most important part, the secondary identification and secondary identifiers. The stored observation in FOD wil be kept for a definite periord of time (like a week, two weeks, a month etc as chosen by the foldscope team). Then they will be identified finally by invited specialists (like students of taxonomy). This permanent/ temporary group is what I call secondary identifiers. They will try to identify the organism upto species or at least genus level (if the genus is big like
 <em>
  navicula
 </em>
 )/ phenomenon. They will try to identify as many organisms/phenomena as they can on that day. It should be a holiday. Then after identification, the observations will be sent to their definite file in FOD and a comment/email/message will be sent to the foldsoper like this: “Final identification of your organism 126000-05-NM in identification request no. 13405 is done. It is
 <em>
  Daptomus Rostripes
 </em>
 . Identification was done by Mr. Z of W university. Identification time : Sunday 12:30 PM”. The secondary identifier can request measurements from the foldscoper and it should be done following the post of @Laks ‘
 <a href="https://microcosmos.foldscope.com/?p=23496">
  Measuring the Foldscope Universe-1: Using the kit scale
 </a>
 ‘. Then he/she will identify it after getting the measurements in next identification session. He/she can add some extra words/information/interesting facts about the organism like it’s a symbiotic animal, it is a vector of a deadly disease destroy it by heating it up to 80°C if you have it, you have discovered a new species! Name it in the new option in your identification request etc. In case of physical phenomenon (as they are rarely seen), the secondary identifiers should be invited after a long interval (like 4-6 months). Thus the final identification is done.
</p>
<p>
 This is my idea regarding the Identification Request system. If you have any better idea, type it down in the comments below so that the foldscope team can see it.
</p>
<p>
 Although doing it may be hard or impossible due to different complexities, there will be a huge database within a few years if it is done. New species can be discovered and foldscope will become more scientific and research oriented.
</p>
<p>
 <em>
  <strong>
   Suggestion 02:
  </strong>
 </em>
</p>
<p>
 There should be options for geo tagging blocks or groups of blocks in a post. Because if one makes a post after gathering several observations from different places, it will create a problem.
</p>
<p>
 <em>
  <strong>
   Suggestion 03:
  </strong>
 </em>
</p>
<p>
 There’s no option to edit your comments in other’s posts but there’s option to edit other’s comments in your post. This should be changed so that one can only edit one’s comments in any post but can not edit other’s comments in one’s posts.
</p>
<p>
 <em>
  <strong>
   Suggestion 04:
  </strong>
 </em>
</p>
<p>
 I think the automatic uploads which are seen while editing a post should be done after 1 minute of inactivity of the editor/foldscoper or before changing website instead of doing it after definite intervals. This shouldn’t interrupt the editing process.
</p>
<p>
 <strong>
  <em>
   Questions:
  </em>
 </strong>
</p>
<ol>
 <li>
  Can 108935-02-AK in ‘
  <a href="https://microcosmos.foldscope.com/?p=108935">
   Old observations
  </a>
  ‘ be
  <em>
   Naegleria fowleri ?
  </em>
 </li>
 <li>
  Is 108935-04-AK diatom in the same post dividing (cell division)?
 </li>
 <li>
  Was there any cell division in the time lapse of meismopedia bacteria in the same post?
 </li>
 <li>
  Can anyone identify the unidentified species in the same post?
 </li>
 <li>
  How to make better ecosystems (in bottles) like in ‘
  <a href="https://microcosmos.foldscope.com/?p=9374">
   Life in a liter of Pond water — Euplotes– Day 1
  </a>
  ‘ and ‘
  <a href="https://microcosmos.foldscope.com/?p=12672">
   Culturing ciliates: The Hay Infusion, Day 8
  </a>
  ‘ with the least amount of death of species?
 </li>
 <li>
  What is 105133-01-AK in the post ‘
  <a href="https://microcosmos.foldscope.com/?p=105133">
   What are these?
  </a>
  ‘ ?
 </li>
 <li>
  Can anyone fufill my wish in the post ‘
  <a href="https://microcosmos.foldscope.com/?p=105762">
   A request
  </a>
  ‘ ?
 </li>
</ol>
<p>
 Please give answers to these in their respective posts.
</p>


Suggestions, Questions.

<p>
 A few days ago I saw a special kind of bacteria called magnetotactic bacteria in the internet. Its a special polyphyletic group of bacteria that orient themselves along the earth’s magnetic field lines. So they can only move north or south in a one dimensional motion. They do this for staying in the zone where there is perfect concentration of oxygen in the pool or water body. They make small crystals of magnetite or gergite in their small organells called magnetosome. They align these crystals to become a mini magnetic compass which can move only north or south. But you can change the direction by taking a magnet near to them. See the video.
</p>
<figure class="wp-block-embed-youtube wp-block-embed is-type-video is-provider-youtube wp-embed-aspect-4-3 wp-has-aspect-ratio">
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   </iframe>
  </div>
 </div>
</figure>
<p>
 Here’s how to extract them:
</p>
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   </iframe>
  </div>
 </div>
</figure>
<p>
 You can control their motion while viewing them under a microscope too. But folscope has two magnets near the place of slide. So the bacteria might just move up and down only which might be a problem to see them. How to solve this problem? Give your ideas in the comments please.
</p>
<p>
 <strong>
  An important thing:
 </strong>
</p>
<p>
 Is 108935-02-AK in my post ‘
 <a href="https://microcosmos.foldscope.com/?p=108935">
  Old observations
 </a>
 ‘ a
 <em>
  Naegleria fowleri
 </em>
 (the brain eating amoeba) or indicate it’s presence? Please check it. Because the water was collected from a pond of saintmartin’s island where many people live and many go to visit every year. I am embedding the video here for you:
</p>
<figure class="wp-block-embed-youtube wp-block-embed is-type-video is-provider-youtube wp-embed-aspect-4-3 wp-has-aspect-ratio">
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   </iframe>
  </div>
 </div>
</figure>
<p>
 Regards
</p>
<p>
 Akib
</p>


A special bacteria and an important thing.

<p>
 I observed a red biofilm in my bottle of chewra dwip algae (which was rotting). I saw many bacterias buzzing around and this event:
</p>
<figure class="wp-block-image">
 <img alt="20190208_225116" class="wp-image-125292 gcloudimg" data-attachment-id="125292" data-comments-opened="1" data-image-meta='{"aperture":"1.9","credit":"","camera":"SM-J700H","caption":"","created_timestamp":"1549666276","copyright":"","focal_length":"3.7","iso":"40","shutter_speed":"0.0075187969924812","title":"","orientation":"6"}' data-image-title="20190208_225116" src="https://storage.googleapis.com/microcosmosdelta.appspot.com/images/transfer_125291/20190208_225116.jpg"/>
 <figcaption>
  Red biofilm 125291-01-AK and bacterias
 </figcaption>
</figure>
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   </iframe>
  </div>
 </div>
 <figcaption>
  A timelapse of the red biofilm.
 </figcaption>
</figure>
<p>
 I seperated a bit of the biofilm and kept it in the slide for a timelapse video. It kinda disintegrated and made a red solution. I will describe it later. But what’s it (rotting)? And what is the red biofilm? Need answers (** note that the red biofilm is probably photosynthetic).
</p>
<p>
 Plus one thing: I suggest @Manu to make a free guide/video tutorial/short video tutorial series for everyone without much delay which will teach them how to identify organisms upto a certain taxonomic level (like class or family) by ownself if making the Identification Request System will take a long time. But if you have already collected the links of posts having identification proplems like this one, you don’t need to make it (please try to keep it in mind that it is almost impossible for one to read all posts even after checking them everyday twice and sorry for too many requests and suggestions!).
</p>
<p>
 Regards
</p>
<p>
 Akib.
</p>
<p>
</p>


What is this phenomenon?

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   </iframe>
  </div>
 </div>
 <figcaption>
  RBCs
 </figcaption>
</figure>
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   <iframe allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="" frameborder="0" height="750" src="https://www.youtube.com/embed/L88Gawq1wno?feature=oembed" width="1000">
   </iframe>
  </div>
 </div>
 <figcaption>
  Platelets?
 </figcaption>
</figure>
<p>
 The blood group is A+ve.
</p>
<p>
 Regards
</p>
<p>
 Akib
</p>


Ali Akib

Earth

Posts

Suggestions, Questions.

A special bacteria and an important thing.

What is this phenomenon?

Blood (From accidental pricking)

What are these?

A request

Old observations

Suggestions, Questions.

A special bacteria and an important thing.

What is this phenomenon?

Blood (From accidental pricking)

What are these?

A request

Old observations

Suggestions, Questions.

A special bacteria and an important thing.

What is this phenomenon?

Blood (From accidental pricking)

Locations

Statistics

Type of Sample

Foldscope Lens Magnification