Paulo's Microscope & Data tips

Source: https://aatventure.news/posts/james-webb-space-telescope-stunning-new-images I like to follow astronomy vlogs and news because I see that many of the technical developments and background theory of this field are often translatable to the parallel world of microscopy.  Around one year ago I stumbled on a youtube video link explaining how digital cameras used in astronomy measure and combine color intensities. I like that the vlogger, the astrophysicist Rebecca Smethurst , manages to explain in a very simple way how CCD cameras work, how light is split through the use of Bayer filters, how the signal intensity in the different parts of the color spectrum is measured  and how these values are combined to form a composite picture. I know that this video is on the field of astronomy, but the technical explanation is well fitting for microscopy as well. I think it is an entry level explanation for students or microscopy enthusiasts in general.  On a side not...

 Hi again! I have been away from the blog for the last weeks because of a small trip to Italy and some days with the flu, but now I am back at posting in this blog. Today's post it is a little tip for Matlab users.  The issue : I have often been confronted with the problem that sometimes I want to access code that is stored in folders and subfolders inside the current folder. Or sometimes I download Github code that has functions stored inside subfolders. I used to avoid organizing and storing my functions inside subfolders because of this problem. Or I would have to find all subfolders and add them to the matlab path one by one.  Solution Today i found out that there is a Matlab function called genpath that generates a list of all subfolders and its children. This can be used to add both the current folder and all subfolders under it to your matlab path. You can check a list of subfolders by using:     P = genpath(mainfolder); or you can add the current folde...

 The news I refer to in this post are not directly associated to optical microscopy, but have to do instead with electron microscopy. A recent article in Nature  reports an increase in resolution up to 1.22 Å with a cryo-EM reconstruction for the human membrane protein   β3 GABA A  receptor homopentamer . This resolution is high enough to find out the individual position of atoms in the protein studied, reports Science . Protein structure has been traditionally mapped by using x-ray crystallography  since the 1950's, but in some cases it is not optimal or even possible to use this technic. These include membrane proteins, very large proteins or proteins associated with ribosomes. On the other hand, cryo-EM only works with a specific type of unusually rigid proteins.    For a longer and deeper read about Cryo-EM technic, follow this link , or the Wikipedia page . 

  The issue : I am not a researcher, although I have been involved in research projects and therefore have a couple of publications published or on the way, as a co-author. Solution : I recently created a page on Research Gate, where the readers can have a look of what have I been working with in the last years. You can see it on the following link: Paulo Girao (researchgate.net) Besides the articles where I am mentioned as a co-author, I have also contributed to designing and programming data analysis tools in the following articles: Organization of Posterior Parietal-Frontal Connections in the Rat - PubMed (nih.gov)  (1) Recurrent inhibitory circuitry as a mechanism for grid formation | Nature Neuroscience  (2) Superficially projecting principal neurons in layer V of medial entorhinal cortex in the rat receive excitatory retrosplenial input - PubMed (nih.gov)  (3) Inhibitory Connectivity Dominates the Fan Cell Network in Layer II of Lateral Entorhinal Cortex - PubM...

  The issue : I have received some comments after my last post where readers have suggested alternative freeware for converting czi to tif files that are not Matlab based. In this post, I will mention some of these.  Alternatives : So, besides the functions I suggested on my last post, here are some alternatives. 1. Horst Obenhaus has suggested a Fiji plugin from Cristopher Leterrier that converts czi files to tif stacks and do some post-processing tasks. You can check the Github link here . The tutorial of how to use this code can be read here . Horst wrote that he has used it, so I see it as a trusted source. 2. Haagen Waade sent me a link to a Github page containing a Python coded czi2tif converter, written in November 2019 by Scott Warchal . I have not and do not know anyone who has tested this code yet, but I am curious to try it. Just by reading the code, I have the impression that it can also batch process czi files in the same directory, so it would make it equival...

The issue : Zeiss czi file format is not always the easiest when thinking of exporting and converting it to other formats. Zeiss provides a free version of their reader called ZEN lite , which permits all users to see and manipulate the acquired images. However, I have often heard users asking me how to convert or export their images into other formats (like TIF). That would make it easier to open and process them in standard commercially available software like Adobe Photoshop, for example. Although possible, this sort of conversion is not simple or straightforward to do when using the different versions of ZEN (black, blue, lite), and they are often different depending on the version. An even harder task is to batch this process, so users would have to repeat the same protocol manually for each file.  Solution : I recently wrote my own pack of functions, collectively called 'czi2tiff' in Matlab, which I now make publicly available at my Github account. The link is:  https://...

 The following article was published yesterday regarding attempts to standardize and find an universal microscopy image format. You can access the article here . The article focus specifically at a format called OME-Zarr, that permits storing big image data in a sort of pyramidal hierarchy, analogous to what is used in algorithms used by Google Earth, for example. You can read the available documentation about this format here . NGFF stands for Next-Generation File Formats.  This theme is not new. You can read about other attempts like OME-TIFF .  A special thanks to Haagen Waade for noticing this article, sharing it with me and editing. 

  The issue : this is a simple issue. I generally open single-leveled TIFF files in Matlab by simply using the function:    data = imread('example.tif'); However, if the tif file in question is multi-layered (3D), this command will only open the top layer and ignore the rest.  Solution : There are two possible solutions for this problem. 1. Using only one command (tested in MatLab R2023, documentation refers to being first released with R2020b):        data  = tiffreadVolume('example.tif'); The numerical array data will therefore have 3 dimensions (x,y,z). I got it automatically in the format uint8 when I tried. Between the two solutions, this one is the fastest. 2. Using multiple lines (maybe for versions prior to MatLab R2020b):      info = imfinfo('example.tif');   data = zeros(info(1).Width,info(1).Height,numel(info)); %preallocates the data array.   data = uint8(data);  %converts the array from double to uin...