Paulo's Microscope & Data tips

 The issue : Many users have complained over the years about the presence of tilling artifacts when they decide to make mosaic images. Namely, it is possible to see lines or boxes through the length and width of the tiled image they acquired. When using brightfield microscopy, this is easily fixed by acquiring an empty image with the same settings of light and focus distance, and then use that image as the reference for shading correction in the program they are using. With fluorescence, this is more complicated because the user needs a fluorescent homogeneous background to focus on. I tried buying fluorescent slides for that purpose, but the results are widely variable, depending on the quality and ease of focus of the slides used.  Solution : I recently acquired calibration beads from Invitrogen ( InSpeck Green Microscope Image Intensity Calibration Kit, wavelength 505/515 nm, 2.5 micrometer size, reference I7219 ) that I was intending to use for another purpose. I generally...

  It has been a while since the last time I had a post on this blog, mostly due to a lot of deadlines to reach related with my work and also due to a couple of accidents that left me bound to my bed/sofa for some weeks in a row. But now I am back! And in 2024, I want to get a deeper look into Laser technology.  On this post I want to share a couple of low-level introductory materials for anyone interested in the history of the invention and development of Laser technology. Laser is the (an)acronym for Light Amplification by Stimulated Emission of Radiation, and it is a relatively recent technology that first saw (or made) light in 1960.  For physics amateurs like myself, I recommend getting a general overview of what a laser is and its properties through reading Jeff Hecht's Understanding Lasers: an Entry Level Guide , or the slightly more advanced Fundamentals of Light Sources and Lasers by Mark Csele.  For an entertaining history of the discovery of the laser, I ...

  The issue : there are different solutions regarding image processing and analysis available, some of them open-sourced, like Fiji/ImageJ , while others are from private companies, like Imaris  or Neurolucida , the later case being more specific for analysis of neuroscience images. Some others are directly connected with big microscopy producers, and in this post I am going to talk about the one that Zeiss chose as their partner, Arivis .  Solution : In the following site , there is the description of an Arivis pipeline that the applications development engineer Dr Kallioupi Arkoudi uses for segmenting and identifying individual neurons. The sample comes from a fixed Thy1-GFP-Mouse brain and the picture was acquired by using a Zeiss LSM 980 laser scanning confocal. The program is modular, in the sense that the user can build his/her own pipeline depending on the type of image or structure they are trying to identify and analyse. From what I understood, there is also an...

  The issue : in my daily work routine, I am constantly bombarded with IT terms like digital processing, algorithm, RAM memory, transistor, CPU, GPU, binary coding, integrated circuit, logical gate, bit depth, etc. With time, you get used to it and get a more or less firm grasp in what these terms mean. But for many years I wondered about how computers actually work, at its most basic level. I felt that this knowledge was lacking for my part and this knowledge gap hindered me from truly understanding the nuances and depths necessary to optimize my use of them. Especially if one is programming.  The solution : Nowadays there are thousands of Youtube videos covering this subject, so it is a matter of sitting down and leap progressively through the different subjects. I can also recommend a Youtube channel called Computerphile  for people who already got the basics and want to understand more about specific concepts or most used algorithms. Nevertheless, for a more traditio...

 I know that this post is a bit off topic regarding the main theme of this blog, but since I work in the field of neuroscience, I thought it could be interesting to some of the readers.  I just found out a very good lecture about the birth of the field of modern neuroscience, where the lecturer, Paolo Mazzarello , tells the story of the life, work and bitter rivalry between the neuroscientists Camillo Golgi and Santiago Ramon y Cajal . They ended up sharing the Nobel Prize in Physiology or Medicine of 1906, "in recognition of their work on the structure of the nervous system". Both have significantly contributed to the contemporary view of neuronal theory. The lecture is, unfortunately, totally in Italian, but if you fall in the skewed intersection of neuroscience nerd and Italian speaker, this lecture is for you. You can find it at this link .  If Italian is not your  forte , you can also see a simplified, shortened, but still entertaining retelling of this st...

Short communication : I recently read that Olympus microscopy section has been rebranded and is now called Evident . It inherits most of the former company, so no radical changes are expected for now. I also got the information that the company just launched its new confocal model, the FV4000 . I was invited to follow a short webinar about their new product at the end of November, so I can write more about the technical innovations of their latest model by then. In the meanwhile, after a quick look at the specifications of the product, it is clear that there is a growing interest, not only from Evident but also from the competitors, in expanding the detection spectrum into the near infrared (NIR). The new model has a detection range from 400 to 900 nm and three extra laser lines (685, 730 and 785 nm). The other technical innovation that sticks out is the use of a new type of detector called SilVIR , and you can read a white paper explaining its properties here .  I promise to write...