Hackuarium - User contributions [en]

20180926 OpenHackuarium 221: DNA Damage Studies

2018-09-27T07:21:15Z

Vithoo:

[[File:Oh221DNA.jpg|200px|thumb|]]
OpenHackuarium #221 - Studies on DNA Damage 
Organisé par Rachel 

'''ENGLISH BELOW''' 
 
* Thème : '''Studies on DNA Damage'''
* Date : '''Mercredi 26.09.2018, 19h''', présentation et discussion à 19:30 et jusqu'à 21h
* Lieu :Salle Gaston Lagaffe, UniverCité, 3ème étage
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
* Main language this week: '''French/English''' 
* Theme: '''Studies on DNA Damage'''
* Date: '''Wednesday 26.09.2018, 19:00''', presentation and discussion start at 19:30
* Location: Room "Gaston Lagaffe", UniverCité, 3rd Floor

== Personnes qui ont prévu de nous présenter quelque chose ==
* [https://www.researchgate.net/profile/Delphine_Plaire Delphine Plaire] will present her experiences studying DNA damage, from irradiation of test animals to comet assays! more info coming soon...
* Additionally, the summer interns, Violaine Regard, Jennifer Veillard, and Vithooban Thavapalan will present short summaries of their results over their 8 weeks in the lab.

== Slides ==
* Do not forget to upload slides before/after the event if appropriate.
Presentation from the summer interns: https://prezi.com/view/PMcwe7vxkdqzS6drJuaS/

== Infos pratiques (plan d'accès etc) ==
cf. [[Open_Hackuarium|#OpenHackuarium]]

== Liens externes & Références ==
*

[[Category:Events]]
[[Category:UpcomingEvents]]
[[Category:OpenHackuarium]]

[[Category:Work In Progress]]

20180926 OpenHackuarium 221: DNA Damage Studies

2018-09-27T07:20:56Z

Vithoo:

[[File:Oh221DNA.jpg|200px|thumb|]]
OpenHackuarium #221 - Studies on DNA Damage 
Organisé par Rachel 

'''ENGLISH BELOW''' 
 
* Thème : '''Studies on DNA Damage'''
* Date : '''Mercredi 26.09.2018, 19h''', présentation et discussion à 19:30 et jusqu'à 21h
* Lieu :Salle Gaston Lagaffe, UniverCité, 3ème étage
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
* Main language this week: '''French/English''' 
* Theme: '''Studies on DNA Damage'''
* Date: '''Wednesday 26.09.2018, 19:00''', presentation and discussion start at 19:30
* Location: Room "Gaston Lagaffe", UniverCité, 3rd Floor

== Personnes qui ont prévu de nous présenter quelque chose ==
* [https://www.researchgate.net/profile/Delphine_Plaire Delphine Plaire] will present her experiences studying DNA damage, from irradiation of test animals to comet assays! more info coming soon...
* Additionally, the summer interns, Violaine Regard, Jennifer Veillard, and Vithooban Thavapalan will present short summaries of their results over their 8 weeks in the lab.

== Slides ==
* Do not forget to upload slides before/after the event if appropriate.
Presentation from the summer interns: [[https://prezi.com/view/PMcwe7vxkdqzS6drJuaS/]]

== Infos pratiques (plan d'accès etc) ==
cf. [[Open_Hackuarium|#OpenHackuarium]]

== Liens externes & Références ==
*

[[Category:Events]]
[[Category:UpcomingEvents]]
[[Category:OpenHackuarium]]

[[Category:Work In Progress]]

Chip for genomic integrity 2018

2018-09-07T12:31:15Z

Vithoo:

This chip prototype is part of the [[Genomic Integrity 2018]].

= Goals =

As many steps of the comet cell assay should be carried out on the chip.
* Concentration of the cells by centrifugation
* Creation of the agarose pads
* Treatment of the agarose pads
* Electrophoresis
* Analyze of the agarose pads

The chip should be easy to produce (either considering the materials we use or the machinery). It should be reusable. As the chip's users won't be used to work in a lab, the chip will need to be easy to use and handle. The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants. We will make various slides, which will need to be changed according to the step.

= Actual design(s) =

== Design 1 (improved) ==

[[File:Design1 07092018.jpg|thumb|upright=1|Design 1 (improved)]]

We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.

''In the end too thick to be observable under a microscope''

=== Concentration of the cells by centrifugation ===
''This step is not implemented in the device yet.''

=== Creation of the agarose pads ===
For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
* The top one contains 6 holes, 2 for each pad (entry and exit hole if overflow). This pads allows to make a really thin pad.
* The middle one is made out of Xerox transparencies paper (ref: 3R96002), and contain three round holes of 15mm diameter for the three pads (Squared pads tend to stick to the walls of the device afterwards)
* The bottom one is a normal slide

=== Treatment of the agarose pads & Electrophoresis ===
After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 20x20mm, larger than the size of a coverslip (otherwise the lasercutter makes them too small). For the electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid.
* One bottom slide with 3 wells of 20x20mm (approximately 3.5mm deep), flanked by small walls (approximately 1.2mm deep, 1x20mm), and on the sides two smaller wells for the electrodes (3.5mm deep, 3x20mm)

Protocol : Put a coverslip in each of the 20x20mm well. Add some liquid on them.
From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette. Do the treatment and then return the whole chip onto a slide and add things through the holes on the sides (electrodes & liquid)

'' Problem: the coverslips do not fall on the slide they stick to the chip''

=== Analyze of the agarose pads ===

Just remove the electrophoresis chip, we should end up with a slide with the pads and coverslips on top.
''Maybe should find a way to dry or change the coverslip before microscope use.''

== Design 2 ==

[[File:DesignV2 07092018.jpg|thumb|upright=1|Design 2 (removable walls)]]

We decided to make the chip larger than the size of a microscope slide (25mm height, 75mm long), as anyway it will be too big to be observable under a microscope.

=== Concentration of the cells by centrifugation ===
''This step is not implemented in the device yet.''

=== Creation of the agarose pads ===
For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
* The top one contains 6 holes, 2 for each pad (entry and exit hole if overflow). This pads allows to make a really thin pad.
* The middle one is made out of Xerox transparencies paper (ref: 3R96002), and contain three round holes of 15mm diameter for the three pads (Squared pads tend to stick to the walls of the device afterwards)
* The bottom one is a normal slide

=== Treatment of the agarose pads & Electrophoresis ===
After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 20x20mm, larger than the size of a coverslip (otherwise the lasercutter makes them too small). For the electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid.
* One bottom slide with 3 wells of 20x20mm (approximately 2.5mm deep), separated by small deeper wells for removable walls (approximately 3.5mm deep, 1.5x26.5mm), and on the sides two smaller wells for the electrodes (2.5mm deep, 3x20mm)

Protocol : Put a slide vertically to make the removable walls. Put a coverslip in each of the 20x20mm well. Add some liquid on them.
From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette. Do the treatment, remove the liquid, remove the walls and add the electrophoresis buffer. Then run the electrophoresis.

=== Analyze of the agarose pads ===

Just remove the electrophoresis chip, we should end up with a slide with the pads and coverslips on top.
''Maybe should find a way to dry or change the coverslip before microscope use.''

= Previous Designs =

== Design 1 ==

We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.
We will make various slides, which will need to be changed according to the step.
The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants.

=== Concentration of the cells by centrifugation ===
''This step is not implemented in the device yet.''

=== Creation of the agarose pads ===
For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
* The top one will contain 6 holes, 2 for each pad (entry and exit hole if overflow)
* The middle one will be thin (if possible 50µm or 100µm thick), and contain three holes of 15x15mm for the three pads
* The bottom one will be a full normal slide

''To check: is the top pad really necessary''

=== Treatment of the agarose pads ===
After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 18x18mm, the size of a coverslip for microscope slide.
* One bottom slide with 3 wells of 18x18mm, 3 times deeper than the agarose pads.

From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette.

''To check: is a top slide needed to perform the treatments''

=== Electrophoresis ===
To make an electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid. The bottom slide for this test is the most complex of our slides.
* One bottom slide with three wells of 18x18mm, XXX µm deep, inside a bigger well less deep XXX µm, flanked by two deeper wells for the electrodes
* One top slide with two holes for the liquid and two for the electrodes. The electrodes will be attached to this slide. The holes will all be above the electrode's wells

Same thing as previous step return the slide containing the pads into this step's bottom slide.

=== Analyze of the agarose pads ===
The 18x18mm wells are the size of a common coverslip. Thus, removing the top of the chip, removing most liquid and adding a coverslip over the three 18x18mm wells should permit the observation of the pads under the microscope.

== Challenges & Problems ==

* The chip does not for the moment enable the concentration of the cells into a small volume. We do perform two centrifugations in the lab, we must see if just letting the cells settle down by gravity would be enough.
* The chip slide would be easily observable under a microscope, but maybe more challenging to do a slide observable with a DIY microscope (like a [[Foldscope]]).
* The chip requires movement of the pads from one slide to another, maybe we should at least label the slides a certain way to make sure not to mix the pads by inadvertence.

File:DesignV2 07092018.jpg

2018-09-07T11:43:42Z

Vithoo:

Chip for genomic integrity 2018

2018-09-07T09:26:56Z

Vithoo:

This chip prototype is part of the [[Genomic Integrity 2018]].

= Goals =

As many steps of the comet cell assay should be carried out on the chip.
* Concentration of the cells by centrifugation
* Creation of the agarose pads
* Treatment of the agarose pads
* Electrophoresis
* Analyze of the agarose pads

The chip should be easy to produce (either considering the materials we use or the machinery). It should be reusable. As the chip's users won't be used to work in a lab, the chip will need to be easy to use and handle.

= Actual design(s) =

== Design 1 (improved) ==

[[File:Design1 07092018.jpg|thumb|upright=1|Design 1 (improved)]]

We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.
We will make various slides, which will need to be changed according to the step.
The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants.

=== Concentration of the cells by centrifugation ===
''This step is not implemented in the device yet.''

=== Creation of the agarose pads ===
For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
* The top one contains 6 holes, 2 for each pad (entry and exit hole if overflow). This pads allows to make a really thin pad.
* The middle one is made out of Xerox transparencies paper (ref: 3R96002), and contain three round holes of 15mm diameter for the three pads (Squared pads tend to stick to the walls of the device afterwards)
* The bottom one is a normal slide

=== Treatment of the agarose pads & Electrophoresis ===
After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 20x20mm, larger than the size of a coverslip (otherwise the lasercutter makes them too small). For the electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid.
* One bottom slide with 3 wells of 20x20mm (approximately 3.5mm deep), flanked by small walls (approximately 1.2mm deep, 1x20mm), and on the sides two smaller wells for the electrodes (3.5mm deep, 3x20mm)

Protocol : Put a coverslip in each of the 20x20mm well. Add some liquid on them.
From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette. Do the treatment and then return the whole chip onto a slide and add things through the holes on the sides (electrodes & liquid)

'' Problem: the coverslips do not fall on the slide they stick to the chip''

=== Analyze of the agarose pads ===

Just remove the electrophoresis chip, we should end up with a slide with the pads and coverslips on top.
''Maybe should find a way to dry or change the coverslip before microscope use.''

== Design 2 ==

[[File:Design1 07092018.jpg|thumb|upright=1|Design 1 (improved)]]

We decided to make the chip larger than the size of a microscope slide (25mm height, 75mm long), as anyway it will be too big to be observable under a microscope.
We will make various slides, which will need to be changed according to the step.
The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants.

=== Concentration of the cells by centrifugation ===
''This step is not implemented in the device yet.''

=== Creation of the agarose pads ===
For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
* The top one contains 6 holes, 2 for each pad (entry and exit hole if overflow). This pads allows to make a really thin pad.
* The middle one is made out of Xerox transparencies paper (ref: 3R96002), and contain three round holes of 15mm diameter for the three pads (Squared pads tend to stick to the walls of the device afterwards)
* The bottom one is a normal slide

=== Treatment of the agarose pads & Electrophoresis ===
After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 20x20mm, larger than the size of a coverslip (otherwise the lasercutter makes them too small). For the electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid.
* One bottom slide with 3 wells of 20x20mm (approximately 3.5mm deep), flanked by small walls (approximately 1.2mm deep, 1x20mm), and on the sides two smaller wells for the electrodes (3.5mm deep, 3x20mm)

Protocol : Put a coverslip in each of the 20x20mm well. Add some liquid on them.
From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette. Do the treatment and then return the whole chip onto a slide and add things through the holes on the sides (electrodes & liquid)

'' Problem: the coverslips do not fall on the slide they stick to the chip''

=== Analyze of the agarose pads ===

Just remove the electrophoresis chip, we should end up with a slide with the pads and coverslips on top.
''Maybe should find a way to dry or change the coverslip before microscope use.''

= Previous Designs =

== Design 1 ==

We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.
We will make various slides, which will need to be changed according to the step.
The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants.

=== Concentration of the cells by centrifugation ===
''This step is not implemented in the device yet.''

=== Creation of the agarose pads ===
For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
* The top one will contain 6 holes, 2 for each pad (entry and exit hole if overflow)
* The middle one will be thin (if possible 50µm or 100µm thick), and contain three holes of 15x15mm for the three pads
* The bottom one will be a full normal slide

''To check: is the top pad really necessary''

=== Treatment of the agarose pads ===
After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 18x18mm, the size of a coverslip for microscope slide.
* One bottom slide with 3 wells of 18x18mm, 3 times deeper than the agarose pads.

From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette.

''To check: is a top slide needed to perform the treatments''

=== Electrophoresis ===
To make an electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid. The bottom slide for this test is the most complex of our slides.
* One bottom slide with three wells of 18x18mm, XXX µm deep, inside a bigger well less deep XXX µm, flanked by two deeper wells for the electrodes
* One top slide with two holes for the liquid and two for the electrodes. The electrodes will be attached to this slide. The holes will all be above the electrode's wells

Same thing as previous step return the slide containing the pads into this step's bottom slide.

=== Analyze of the agarose pads ===
The 18x18mm wells are the size of a common coverslip. Thus, removing the top of the chip, removing most liquid and adding a coverslip over the three 18x18mm wells should permit the observation of the pads under the microscope.

== Challenges & Problems ==

* The chip does not for the moment enable the concentration of the cells into a small volume. We do perform two centrifugations in the lab, we must see if just letting the cells settle down by gravity would be enough.
* The chip slide would be easily observable under a microscope, but maybe more challenging to do a slide observable with a DIY microscope (like a [[Foldscope]]).
* The chip requires movement of the pads from one slide to another, maybe we should at least label the slides a certain way to make sure not to mix the pads by inadvertence.

File:Design1 07092018.jpg

2018-09-07T09:12:54Z

Vithoo:

DIY Fluorescence Microscope

2018-09-04T13:42:22Z

Vithoo: /* Material Used */

In order to observe the result from the [[Comet Cell Assay 2018]], SYBRsafe is added to color the tails. Before the observation of fluorescent process was not possible in the hacker space. It was thus decided to transform one of the microscope into a fluorescent microscope.

==Biological Background==

This dye is a epifluorescent one.(?) The molecules are excited when they receive a given wavelength (all wavelength < 509) and in reaction they emit another wavelength (524 nm).

==Material Used==

We get inspiration from the [[Diy-transilluminator]]. We observe that this equipment allows us to observe reactions done with the SYBRsafe (?) and thus decided to mimic it. In short, blue LEDs are used for the excitation part. Then a yellow lens is added to remove specific wavelength and keep only that one of interest.

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

===Available Code===

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

DIY Fluorescence Microscope

2018-09-04T13:41:37Z

Vithoo: /* Material Used */

In order to observe the result from the [[Comet Cell Assay 2018]], SYBRsafe is added to color the tails. Before the observation of fluorescent process was not possible in the hacker space. It was thus decided to transform one of the microscope into a fluorescent microscope.

==Biological Background==

This dye is a epifluorescent one.(?) The molecules are excited when they receive a given wavelength (all wavelength < 509) and in reaction they emit another wavelength (524 nm).

==Material Used==

We get inspiration from the DIY Gel Transiluminator build by the GaudiLabs. ([[Diy-transilluminator]]) We observe that this equipment allows us to observe reactions done with the SYBRsafe (?) and thus decided to mimic it. In short, blue LEDs are used for the excitation part. Then a yellow lens is added to remove specific wavelength and keep only that one of interest.

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

===Available Code===

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

DIY Fluorescence Microscope

2018-09-04T13:41:15Z

Vithoo: /* Material Used */

In order to observe the result from the [[Comet Cell Assay 2018]], SYBRsafe is added to color the tails. Before the observation of fluorescent process was not possible in the hacker space. It was thus decided to transform one of the microscope into a fluorescent microscope.

==Biological Background==

This dye is a epifluorescent one.(?) The molecules are excited when they receive a given wavelength (all wavelength < 509) and in reaction they emit another wavelength (524 nm).

==Material Used==

We get inspiration from the DIY Gel Transiluminator build by the GaudiLabs. (http://wiki.hackuarium.ch/w/Diy-transilluminator) We observe that this equipment allows us to observe reactions done with the SYBRsafe (?) and thus decided to mimic it. In short, blue LEDs are used for the excitation part. Then a yellow lens is added to remove specific wavelength and keep only that one of interest.

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

===Available Code===

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

Genomic Integrity 2018

2018-09-04T13:23:56Z

Vithoo:

Kitchen-sink-ingredients

2018-09-04T13:22:40Z

Vithoo:

The most difficult objective is to find usual ingredients that can be easily found to replace the different chemicals needed for the experiment. We did not have enough time to study this precisely but still were able to compare the results of the experiment done in different conditions.

==Sterile vs Bidistilled water==

==Methylene blue rather than SYBRsafe==

The first target was SYBR Safe.<ref>[https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/dna-stains/sybr-safe.html ThermoFischer's documentations for SYBR Safe]. Retrieved 27 August 2018.</ref> Even though SYBR Safe is far less toxic than Ethidium Bromide, SYBR Gold or other fluorescent dyes, it has not zero toxicity. By its mode of action (intercalation), it can be carcinogenic and the obligation to use a specific light (here a powerful blue light) is an obstacle for easy procedures and it can cause harm to the eyes of the user. 

Therefore, we wanted to use Methylene Blue.<ref>[https://en.wikipedia.org/wiki/Methylene_blue Wikipedia page for Methylene Blue]. Retrieved 27 August 2018.</ref> As it is positively charged, it will bind to the outside structure of the DNA, without intercalating within it and without triggering much mutation. Plus, Methylene Blue is easy to find (it is on the WHO's list of essential medicines). Whereas for the Micronuclei Assay the methylene blue worked well, for the Comet Assay methylene blue did not give satisfactory results. 

Photos of comet 

==References==
<references />

Kitchen-sink-ingredients

2018-09-04T13:22:18Z

Vithoo: /* Methylene blue rather than SYBRsafe */

Genomic Integrity 2018

2018-09-04T13:22:09Z

Vithoo: /* Procedure */

Kitchen-sink-ingredients

2018-09-04T13:18:58Z

Vithoo: Created page with "The most difficult objective is to find usual ingredients that can be easily found to replace the different chemicals needed for the experiment. We did not have enough time to..."

DIY Fluorescence Microscope

2018-09-04T13:18:06Z

Vithoo:

In order to observe the result from the [[Comet Cell Assay 2018]], SYBRsafe is added to color the tails. Before the observation of fluorescent process was not possible in the hacker space. It was thus decided to transform one of the microscope into a fluorescent microscope.

==Biological Background==

This dye is a epifluorescent one.(?) The molecules are excited when they receive a given wavelength (all wavelength < 509) and in reaction they emit another wavelength (524 nm).

==Material Used==

We get inspiration from the DIY Gel Transiluminator build by the GaudiLabs. We observe that this equipment allows us to observe reactions done with the SYBRsafe (?) and thus decided to mimic it. In short, blue LEDs are used for the excitation part. Then a yellow lens is added to remove specific wavelength and keep only that one of interest.

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

===Available Code===

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

Genomic Integrity 2018

2018-09-04T08:36:34Z

Vithoo:

Summer 2018 Genomic Integrity Project.

==Issue==
Assessing genomic integrity (showing the amount of damage one's genome has endured) would be of a great help for public health. Unfortunately, the tests allowing to check the genomic integrity can be complex or expensive.

==Objectives==
Therefore, the objectives of this internship would be:
* To make a ready to use device: [[Chip for genomic integrity 2018]], the best being automatic, for people (even non-scientist) to use easily;
* To use "[[kitchen-sink-ingredients]]" to promote easy to do and safe citizen science;
* Finally, to develop an [[Automatic Cell Counter Algorithm]] able to count cells and control different parameters (their sizes, the length of their comet tails and recognition of micronuclei). 

Asides Objectives
* To use a Foldscope<ref>[https://www.foldscope.com/ Official website of the Foldcope].Retrieved 2 August 2018.</ref> <ref>[http://wiki.hackuarium.ch/w/Foldscope Wiki of the hackuarium].Retrieved 28 August 2018.</ref> or a microscope to make photos with a RaspBerry Pi, using an [[automatic stage]];
* [[DIY Fluorescence Microscope]]

==Procedure==
Precisely, we will use two methods [[Micronuclei Assay 2018]] and [[Comet Cell Assay 2018]], find a way to make the procedures as simple as possible using a chip and make an algorithm to handle the results. 

For both, we tried to replace all the toxic or hard to find components by "[[kitchen-sink-ingredients]]", in order to make this technique widely usable by anyone, even without the appropriate equipment. 

The first target was SYBR Safe.<ref>[https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/dna-stains/sybr-safe.html ThermoFischer's documentations for SYBR Safe]. Retrieved 27 August 2018.</ref> Even though SYBR Safe is far less toxic than Ethidium Bromide, SYBR Gold or other fluorescent dyes, it has not zero toxicity. By its mode of action (intercalation), it can be carcinogenic and the obligation to use a specific light (here a powerful blue light) is an obstacle for easy procedures and it can cause harm to the eyes of the user. 

Therefore, we wanted to use Methylene Blue.<ref>[https://en.wikipedia.org/wiki/Methylene_blue Wikipedia page for Methylene Blue]. Retrieved 27 August 2018.</ref> As it is positively charged, it will bind to the outside structure of the DNA, without intercalating within it and without triggering much mutation. Plus, Methylene Blue is easy to find (it is on the WHO's list of essential medicines). Whereas for the Micronuclei Assay the methylene blue worked well, for the Comet Assay methylene blue did not give satisfactory results. 

Photos of comet 

==Protocol==
''For the detailed protocol, see [[Step by step protocol for comet assay]]''

==References==
<references />

DIY Fluorescence Microscope

2018-09-04T08:33:01Z

Vithoo:

Before the observation of fluorescent process was not possible in the hacker space. It was thus decided that transforming one of the microscope into a fluorescent microscope would be cool.

==Background and Procedure==

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

===Available Code===

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

DIY Fluorescence Microscope

2018-09-04T08:31:48Z

Vithoo: /* No more used */

Before the observation of fluorescent process was not possible in the hacker space. It was thus decided that transforming one of the microscope into a fluorescent microscope would be cool.

==Background and Procedure==

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

==Available Code==

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

DIY Fluorescence Microscope

2018-09-04T08:31:28Z

Vithoo:

Before the observation of fluorescent process was not possible in the hacker space. It was thus decided that transforming one of the microscope into a fluorescent microscope would be cool.

==Background and Procedure==

==Results ==

===Overlay===

Fluorescence is visible through the Raspberry Pi Camera. An idea then is to implement a code to overlay the picture of the cell and the fluorescent picture. The goal of this overlay would be to confirm that the fluorescence comes from the nucleus.

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:16-29-06.jpg|Phase
File:16-28-53.jpg|Fluo
File:Overlay1.png|Overlay
</gallery>

<gallery perrow="5" mode="packed" widths="px" heights="px">
File:17-12-10.jpg|Phase
File:17-12-32.jpg|Fluo
File:Overlay2.png|Overlay
</gallery>

===Idea to improve the result===

We observe that the resulting "phase" image in yellowish, this is due to the yellow lens that have been added. An idea would be to remove this lens to take the "phase" picture and add it only for the "fluo" one.

==Available Code==

==No more used==

This microscope works well to observe fluorescent nucleus but its resolution is not enough to observe comets. Thus it could not be used to assess the [[Comet Cell Assay 2018]].

DIY Fluorescence Microscope

2018-09-04T08:15:24Z

Vithoo: /* Results */

DIY Fluorescence Microscope

2018-09-04T08:13:15Z

Vithoo: /* Results */

File:16-28-53.jpg

2018-09-04T08:12:56Z

Vithoo:

DIY Fluorescence Microscope

2018-09-04T08:12:37Z

Vithoo: /* Results */

DIY Fluorescence Microscope

2018-09-04T08:12:07Z

Vithoo: /* Results */

File:16-29-06.jpg

2018-09-04T08:11:49Z

Vithoo:

DIY Fluorescence Microscope

2018-09-04T08:10:55Z

Vithoo: /* Results */

File:17-12-10.jpg

2018-09-04T08:10:41Z

Vithoo:

DIY Fluorescence Microscope

2018-09-04T08:10:17Z

Vithoo: /* Results */

File:17-12-32.jpg

2018-09-04T08:09:49Z

Vithoo:

File:Overlay2.png

2018-09-04T08:07:30Z

Vithoo:

DIY Fluorescence Microscope

2018-09-04T08:07:14Z

Vithoo: /* Results */

File:Overlay1.png

2018-09-04T08:06:49Z

Vithoo:

DIY Fluorescence Microscope

2018-09-04T08:03:32Z

Vithoo: Created page with "Before the observation of fluorescent process was not possible in the hacker space. It was thus decided that transforming one of the microscope into a fluorescent microscope w..."

Genomic Integrity 2018

2018-09-04T07:59:41Z

Vithoo: /* Objectives */

Summer 2018 Genomic Integrity Project.

==Issue==
Assessing genomic integrity (showing the amount of damage one's genome has endured) would be of a great help for public health. Unfortunately, the tests allowing to check the genomic integrity can be complex or expensive.

==Objectives==
Therefore, the objectives of this internship would be:
* To make a ready to use device, the best being automatic, for people (even non-scientist) to use easily;
* To use "[[kitchen-sink-ingredients]]" to promote easy to do and safe citizen science;
* Finally, to develop an [[Automatic Cell Counter Algorithm]] able to count cells and control different parameters (their sizes, the length of their comet tails and recognition of micronuclei). 

Asides Objectives
* To use a Foldscope<ref>[https://www.foldscope.com/ Official website of the Foldcope].Retrieved 2 August 2018.</ref> <ref>[http://wiki.hackuarium.ch/w/Foldscope Wiki of the hackuarium].Retrieved 28 August 2018.</ref> or a microscope to make photos with a RaspBerry Pi, using an [[automatic stage]];
* [[DIY Fluorescence Microscope]]

==Procedure==
Precisely, we will use two methods [[Micronuclei Assay 2018]] and [[Comet Cell Assay 2018]], find a way to make the procedures as simple as possible using a chip and make an algorithm to handle the results. 

For both, we tried to replace all the toxic or hard to find components by "[[kitchen-sink-ingredients]]", in order to make this technique widely usable by anyone, even without the appropriate equipment. 

The first target was SYBR Safe.<ref>[https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/dna-stains/sybr-safe.html ThermoFischer's documentations for SYBR Safe]. Retrieved 27 August 2018.</ref> Even though SYBR Safe is far less toxic than Ethidium Bromide, SYBR Gold or other fluorescent dyes, it has not zero toxicity. By its mode of action (intercalation), it can be carcinogenic and the obligation to use a specific light (here a powerful blue light) is an obstacle for easy procedures and it can cause harm to the eyes of the user. 

Therefore, we wanted to use Methylene Blue.<ref>[https://en.wikipedia.org/wiki/Methylene_blue Wikipedia page for Methylene Blue]. Retrieved 27 August 2018.</ref> As it is positively charged, it will bind to the outside structure of the DNA, without intercalating within it and without triggering much mutation. Plus, Methylene Blue is easy to find (it is on the WHO's list of essential medicines). Whereas for the Micronuclei Assay the methylene blue worked well, for the Comet Assay methylene blue did not give satisfactory results. 

Photos of comet 

==Protocol==
''For the detailed protocol, see [[Step by step protocol for comet assay]]''

==Ready to use chip==
''Detailed article: [[Chip for genomic integrity 2018]] ''

==References==
<references />

Automatic Cell Counter Algorithm

2018-09-04T07:46:11Z

Vithoo: /* Pre-processing */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some pre-processing instead of directly searching for cells contour.

The pre-processing will mainly remove noise due to the difference in luminosity. In addition it will ignore the durst that is present in both images. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing is easier if the field of view is the same on all images (same luminosity). Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.
Another method was then tested, the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:45:35Z

Vithoo: /* Pre-processing */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some pre-processing instead of directly searching for cells contour.

The pre-processing will mainly remove noise due to the difference in luminosity. In addition it will ignore the durst that is present in both images. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing is easier if the field of view is the same on all images (same luminosity). Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:45:20Z

Vithoo: /* Picture Procedure */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some pre-processing instead of directly searching for cells contour.

The pre-processing will mainly remove noise due to the difference in luminosity. In addition it will ignore the durst that is present in both images. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing is easier if the field of view is the same on all images (same luminosity). Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:43:31Z

Vithoo: /* Picture Procedure */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some pre-processing instead of directly searching for cells contour.

The pre-processing will mainly remove noise due to the difference in luminosity. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:43:00Z

Vithoo: /* Picture Procedure */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

The pre-processing will mainly remove noise due to the difference in luminosity. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:41:02Z

Vithoo: /* Picture Procedure */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. The pre-processing will also remove noise due to the difference in luminosity. This removal would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:38:21Z

Vithoo: /* Picture Procedure */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:37:18Z

Vithoo: /* Picture Procedure */

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-04T07:35:58Z

Vithoo:

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, the cells were quite difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-03T15:25:59Z

Vithoo:

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this would be easy as the micronuclei would also be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, the cells were quite difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

===Results===
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

==Available Code==

Automatic Cell Counter Algorithm

2018-09-03T15:23:46Z

Vithoo: /* Cell Selection */

Automatic Cell Counter Algorithm

2018-09-03T15:23:26Z

Vithoo:

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this would be easy as the micronuclei would also be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, the cells were quite difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

===Pre-processing===

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

===Cell Selection===

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

Results:
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

Automatic Cell Counter Algorithm

2018-09-03T15:20:40Z

Vithoo:

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this would be easy as the micronuclei would also be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, the cells were quite difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

Results:
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:Screen Shot 2018-09-03 at 17.19.26.png|Groups of Cells Detection
</gallery>

==Nucleus Detection==

File:Screen Shot 2018-09-03 at 17.19.26.png

2018-09-03T15:20:06Z

Vithoo:

Automatic Cell Counter Algorithm

2018-09-03T15:18:54Z

Vithoo:

The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this would be easy as the micronuclei would also be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be to distinguish micronuclei from those other elements.

==Background and Material Used==

Methylene blue is known as a DNA dye. Thus it enable to discriminate the nucleus from the rest of the cell. This dye is widely used and allow a quite good visual recognition. Micronuclei, which is also composed of DNA, will also be coloured by this dye.

Pictures used to build the algorithm are taken using the Raspberry Pi Camera connected to the microscope.

==Picture Procedure ==

First, we took photos while zooming on the cells of interest. As cells are quite translucent, the cells were quite difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.

In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:10-12-46.jpg|Cell
File:10-14-05.jpg|Background
</gallery>

==Cell Detection==

Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.

Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Substraction.png|Subtraction Method
File:Difference.png|Difference Method
</gallery>

Cell selection is done as followed:
* First contours on the difference image are computed.
* Then a thresholding step is done in order to keep only larger contours (larger area), the ones that may represent cells.
* Finally, the nucleus detection (next step) will be done on those larger contours only.

Results:
The developed algorithm is able to find isolated cells as well as groups of cells. Then a mask is applied in order to keep only what is inside the cells. This would simplify the next step which is finding the nucleus.

<gallery perrow="4" mode="packed" widths="px" heights="px">
File:Screen Shot 2018-08-09 at 10.18.07.png|Single Cell Detection
File:10-14-05.jpg|Groups of Cells Detection
</gallery>

==Nucleus Detection==

File:Difference.png

2018-09-03T15:18:36Z

Vithoo: