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GMU:Introduction to Microscopy/Denise Nicoau (view source)
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* Sterile environment (petri dish or bigger container) | * Sterile environment (petri dish or bigger container) | ||
* Don't feed it at the beginning | * Don't feed it at the beginning | ||
* Give it just 1 oat meal per when it starts growing/moving, if you feed it too much (lots of oat meals) it will become moldy fast; when it is big enough you can give it more oats meal | * Give it just 1 oat meal per day when it starts growing/moving, if you feed it too much (lots of oat meals) it will become moldy fast; when it is big enough you can give it more oats meal | ||
* Don't forget about your slim mold! If you forget about it for a couple of days, it will be moldy. | * Don't forget about your slim mold! If you forget about it for a couple of days, it will be moldy. | ||
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'''Photoshop editing''' | '''Photoshop editing''' | ||
Below some artworks I created starting from some microscope pictures I've taken by simply changing some adjustments or overlap pictures on Photoshop. | |||
[[File:exp1-dn.png|300px]] | [[File:exp1-dn.png|300px]] | ||
[[File:mush5.png|300px]] | [[File:mush5.png|300px]] | ||
[[File:mush9.png|300px]] | [[File:mush9.png|300px]] | ||
[[File:mush6.png|300px]] | |||
[[File:mush7-dn.png|300px]] | |||
[[File:mush3.png|300px]] | [[File:mush3.png|300px]] | ||
[[File:mush8.png|300px]] | [[File:mush8.png|300px]] | ||
[[File:worm3.png|300px]] | [[File:worm3.png|300px]] | ||
''11/12/2020'' | |||
Today I went to the BioLAB and I examined some samples collected 2 days ago. I picked some muddy water and muddy/wet leaves samples, added some water drops, shake them a bit and and left them in the lab. | |||
2 days ago I collected some compost and soil as well but I couldn't examine them, time flies! | |||
Sascha kindly lent me his camera to film some little organisms moving in my specimens. It was funny, but also super hard to keep focused the area, in fact we figured out that the focus seen by the eye through the eye-lens is different from the output show by the camera. Below what I found. | |||
''Wet/muddy leaves'' | |||
<gallery> | |||
File:Wet-leaves1.jpg | |||
File:Wet-leaves2.jpg | |||
File:Wet-leaves3.jpg | |||
File:Wet-leaves4.jpg | |||
File:Wet-leaves5.jpg | |||
File:Wet-leaves7.jpg | |||
File:Wet-leaves8.jpg | |||
File:Wet-leaves9.jpg | |||
</gallery> | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf wet leaves - camera documentation] | |||
''Muddy water'' | |||
<gallery> | |||
File:muddy1.jpg | |||
File:muddy2.jpg | |||
File:muddy3.jpg | |||
File:muddy4.jpg | |||
File:muddy5.jpg | |||
File:muddy6.jpg | |||
File:muddy7.jpg | |||
</gallery> | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf muddy water - phone documentation] | |||
'''Slime mold''' | |||
I also prepared in 2 new (not contaminated) petri dishes the ultimate environment for cultivating slime molds (Agar powder + water mixed together and heat up in the microwave) and put 1 oat flake with a part of a slim mold over it in the first petri dish and 2 oak flakes with 2 different slime molds over them in the second dish. | |||
The slime molds were already alive from the previous 'dry' condition so that I could feed them with a few oat flakes. | |||
''13/12/2020'' | |||
Below the progress of my slime molds I am cultivating. | |||
''Condition: closed petri dish with agar, inside a shoes box.'' | |||
''SLIME MOLD 1'' | |||
<gallery> | |||
File:slime2-2.jpg | DAY 2 | |||
File:slime2-3.jpg | DAY 3 - 11:00 | |||
File:slime2-4.jpg | DAY 3 - 23:52 | |||
File:slime2-5.jpg | DAY 4 | |||
</gallery> | |||
''SLIME MOLD 2'' | |||
<gallery> | |||
File:slime1-1.jpg | DAY 1 | |||
File:slime1-3.jpg | DAY 2 | |||
File:slime1-4.jpg | DAY 3 - 11:00 | |||
File:slime1-5.jpg | DAY 3 - 23:52 | |||
File:slime1-6.jpg | DAY 4 | |||
</gallery> | |||
After 4 days this is the condition of my slime molds (no mold found): | |||
[[File:slime-together-dn.jpg|400px]] | |||
==|'''WEEK SEVEN'''|== | |||
''16/12/2020'' | |||
I was intended to examine through the microscope the compost sample collected in the bottom of my kitchen bin. It was a mixture of topsoil, onion and tangerine skin, shook it with some water drops and left for almost a week in the lab. Unfortunately, we are in a total lockdown from today, therefore I will not have access to the BioLab. | |||
''17/12/2020'' | |||
'''Slime mold''' | |||
For what concerns my slime molds I created a new environment with water and agar in a new petri dish, attached to the original one, in order to let my slim mold move to the new environment, creating a bridge. I informed myself about how to cultivate a slime mold creating an ultimate environment for her, and one of the main rules consists in keep the environment clean in order to prevent mold. | |||
In doing so I had to keep the petri dishes open, inside of the shoe box, but after some days I found out a little moldy dark spot growing in the agar. I removed it and give my slime molds to Sisu because tomorrow I will leave Weimar coming back home for Christmas Holidays. | |||
Below the progress. | |||
''SLIME MOLD 1'' | |||
I set the new environment to let her create a bridge, but it was growing super fast in the opposite direction. (Maybe it felt the new petri dish like a dirty one and not appealing anymore) | |||
<gallery> | |||
File:slime1-dn.jpg | DAY 6 | |||
File:slime1-2dn.jpg | DAY 8 | |||
File:slime1-3dn.jpg | DAY 9 | |||
</gallery> | |||
[[File:slime1-3dn.jpg|400px]] | |||
''SLIME MOLD 2'' | |||
I set the new environment to let her create a bridge, but after one day open I decided to close the petri dish and put one oat flake in the other new dish, closed. Hence, I dropped the idea of the bridge for this slime mold and I didn't feed it for one whole day: the slime mold was escaping looking for food, you can see it from the growth on the walls of the petri dish. | |||
<gallery> | |||
File:slime2-dn.jpg | DAY 6 | |||
File:slime2-2dn.jpg | DAY 7 | |||
File:slime2-3dn.jpg | DAY 8 | |||
File:slime2-4dn.jpg | DAY 9 | |||
</gallery> | |||
[[File:slime2-3dn.jpg|400px]] | |||
''SLIME MOLD 3'' | |||
The oat flake taken from slide mold 2, put in a new petri dish (left open for a day) | |||
[[File:slime3-1.jpg|400px|DAY 2]] | |||
==|'''WEEK EIGHT'''| & |'''WEEK NINE'''|== | |||
'''Slime mold''' | |||
I left Weimar for Christmas break. But I want to show some slime mold pictures under the microscope that I personally took in the Biolab after some days of them growing. I think they are pretty amazing. | |||
<gallery> | |||
File:slimemold1.jpg | |||
File:slimemold2.jpg | |||
File:slimemold3.jpg | |||
File:slimemold4.jpg | |||
File:slimemold6.jpg | |||
File:slimemold7.jpg | |||
File:slimemold8.jpg | |||
File:slimemold9.jpg | |||
File:slimemold10.jpg | |||
File:slimemold11.jpg | |||
File:slimemold12.jpg | |||
File:slimemold13.jpg | |||
File:slimemold14.jpg | |||
File:sls.jpg | |||
File:slimemold15.jpg | |||
File:slimemold16.jpg | |||
File:slimemold17.jpg | |||
File:slimemold18.jpg | |||
File:slimemold19.jpg | |||
File:slimemold20.jpg | |||
File:slimemold21.jpg | |||
File:slimemold22.jpg | |||
File:slimemold23.jpg | |||
File:slimemold24.jpg | |||
File:slimemold25.jpg | |||
File:slimemold27.jpg | |||
File:slimemold28.jpg | |||
File:slimemold29.jpg | |||
File:slimemold30.jpg | |||
File:slimemold31.jpg | |||
File:slimemold32.jpg | |||
File:slimemold33.jpg | |||
File:slimemold34.jpg | |||
File:slimemold35.jpg | |||
File:slimemold36.jpg | |||
File:slimemold37.jpg | |||
File:slimemold38.jpg | |||
File:slimemold39.jpg | |||
File:slimemold40.jpg | |||
File:slimemold41.jpg | |||
File:slimemold42.jpg | |||
File:slimemold43.jpg | |||
File:slimemold44.jpg | |||
File:slimemold45.jpg | |||
File:slimemold46.jpg | |||
File:slimemold47.jpg | |||
File:slimemold48.jpg | |||
File:slimemold49.jpg | |||
</gallery> | |||
==='''AI generated images'''=== | |||
I collected many microscopy pictures so far. I have a dataset of more than 2300 images. I decided to lend a new slant to this project, moving from analog to digital. | |||
I worked with an online software which takes advantage of machine learning (to be more precise StyleGan2) to synthetise new data starting from a massive dataset. Hence, I trained several different machine learning models started from different pre-trained dataset to start learning from, and then added my original microscopy dataset. | |||
I selected a parameter called '''steps''' which influences in a significant way the training process: it establishes the number of steps the model has to go through, so the timing required (of course the more it works the better.) | |||
---- | |||
--- | |||
'''1st attempt''' 3000 steps | |||
--- | |||
[[File:steps-1st-attemp.mp4]] | |||
Here I started from a pre-trained dataset of HQ landscapes and then selected my first microscopy dataset as custom dataset. The first dataset was based on less images - about 1200 - therefore I got as a result a less heterogeneous folder of images. | |||
Output and notes: | |||
1000 new samples images generated by this machine learning model which look like my images (although not that similar because based on an indefinite shape; this feature comes from the fact that my original images where quite blurred and dark, in fact my initial aim was to create analog errors! It is pretty amazing how the algorithm works in trying to reproduce the input). | |||
Preview generated folder: | |||
<gallery> | |||
File:img000000002.jpg | |||
File:img000000015.jpg | |||
File:img000000034.jpg | |||
File:img000000058.jpg | |||
File:img000000064.jpg | |||
File:img000000065.jpg | |||
File:img000000128.jpg | |||
File:img000000171.jpg | |||
File:img000000146.jpg | |||
File:img000000529.jpg | |||
File:img000000723.jpg | |||
File:img000000816.jpg | |||
</gallery> | |||
---- | |||
--- | |||
'''2nd attempt''' 7000 steps | |||
--- | |||
[[File:steps-dataset2-microscopy-2ndattempt - Progress Video.mp4]] | |||
Here I started from a pre-trained dataset of HQ landscapes and then selected my second microscopy dataset as custom one. The second dataset was based on more images - 2300 - therefore I got as a result a more heterogeneous folder of images. | |||
Output and notes: | |||
1000 new samples images generated by this machine learning model which look like my images (they still have indefinite shapes instead of rounded ones, but they are more colorful and diverse); | |||
Preview generated folder: | |||
<gallery> | |||
File:img000000000.jpg | |||
File:img000000006.jpg | |||
File:img000000003.jpg | |||
File:img000000005.jpg | |||
File:img000000030.jpg | |||
File:img000000018.jpg | |||
File:img000000044.jpg | |||
File:img000000088.jpg | |||
File:img000000095.jpg | |||
File:img000000001.jpg | |||
File:img000000205.jpg | |||
File:img000000180.jpg | |||
</gallery> | |||
---- | |||
--- | |||
'''3rd attempt''' 700 steps | |||
--- | |||
[[File:dataset-3-microscopy-dn - Progress Video.mp4]] | |||
Here I decided to change the pre-trained dataset with far away data in order to see what could have happened with something that different from the original images. Therefore, I used a pre-trained dataset of HQ faces and then selected the 2nd part of the microscope images I took - about 1100 - as custom dataset. | |||
Output and notes: | |||
This model training process failed at some point (700 steps rather than 2000 set), but it worked however. | |||
500 new samples images generated by this machine learning model which look like my images (they still have indefinite shapes instead of rounded ones, but they are more colorful and diverse); | |||
Preview generated folder: | |||
<gallery> | |||
File:gifedwd.jpg | |||
File:gifedwd1.jpg | |||
File:gifedwd2.jpg | |||
File:gifedwd3.jpg | |||
File:gifedwd4.jpg | |||
File:gifedwd5.jpg | |||
File:gifedwd6.jpg | |||
File:gifedwd7.jpg | |||
File:gifedwd16.jpg | |||
File:gifedwd62.jpg | |||
File:gifedwd99.jpg | |||
File:v25.jpg | |||
</gallery> | |||
---- | |||
--- | |||
'''4th attempt''' 8000 steps: | |||
--- | |||
[[File:Training Image Experiment on mycroscope - Progress Video.mp4]] | |||
Here I decided to change the pre-trained dataset with closer data in order to see whether I could get an improvement. Therefore, I used the 1st folder generated by the ML model as pre-trained dataset and then selected the complete microscope dataset as custom one. | |||
Output and notes: | |||
1000 new samples images generated by this machine learning model which are really similar to my original images, rounded and detailed. | |||
Preview generated folder: | |||
<gallery> | |||
File:gdeiugcf.jpg | |||
File:hbwhjdbw08.jpg | |||
File:hbwhjdbw12.jpg | |||
File:hbwhjdbw26.jpg | |||
File:hbwhjdbw44.jpg | |||
File:hbwhjdbw49.jpg | |||
File:hbwhjdbw50.jpg | |||
File:hbwhjdbw67.jpg | |||
File:hbwhjdbw82.jpg | |||
File:hbwhjdbw134.jpg | |||
File:hbwhjdbw187.jpg | |||
File:hbwhjdbw721.jpg | |||
</gallery> | |||
---- | |||
Now I am trying to create some videos by shaping interpolation on the latent space, so smooth transitions between one generated picture and another, with different soundtracks under them. | |||
==|'''WEEK TEN'''|== | |||
''07/01/2021'' | |||
Some of the interpolation videos I made with different soundtracks over: | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Video1-bauhaus] | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Video2-teebs] | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Video3-nude] | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Video4-robotics] | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Video5-robotics] | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Video6-sadwhales] | |||
==|'''WEEK ELEVEN'''|== | |||
''12/01/2021'' | |||
I made two others interpolation videos putting as a soundtrack a BBC documentary: | |||
1st: [https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Blue Planet] | |||
2nd: [https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Black Holes] | |||
''15/01/2021'' | |||
My collection of videos is done. I thought it was nice to create a loop video with some of the interpolations playing together all in once, and so I did > [https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos Loop Interpolation Videos] | |||
==|'''WEEK TWELVE'''|== | |||
''18/01/2021'' | |||
I edited two videos in speed and sound, adjusting some parameters to better match visual and sound: | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos black holes] | |||
[https://cloud.uni-weimar.de/s/46XRnyKLwBsG9cf?path=%2Fdenise%20nicolau%2FML-videos blue planet 2] | |||
''20/01/2021'' | |||
I am creating a narrative that connects each video avoiding the linear common sense, in favor of dizzying the spectator. \WORK IN PROGRESS\ | |||
==|'''WEEK THIRTEEN & FOURTEEN'''|== | |||
''03/02/2021'' | |||
The final narrative is ready here: [https://www.youtube.com/watch?v=awOCMRase8s&ab_channel=DeniseNicolau Echoes] | |||