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  • Feb 26 18:45
    GitLab | Julian Stirling pushed 1 commits to openflexure-microscope
  • Feb 25 15:39
    GitLab | Joe Knapper pushed to openflexure-microscope
  • Feb 25 15:39
    GitLab | Joel Collins pushed 4 commits to openflexure-microscope
  • Feb 21 15:23
    GitLab | Joe Knapper pushed to openflexure-microscope
  • Feb 21 15:23
    GitLab | Joel Collins pushed 4 commits to openflexure-microscope
  • Feb 21 13:21
    GitLab | Joe Knapper pushed 1 commits to openflexure-microscope
  • Feb 19 19:56
    GitLab | Julian Stirling pushed to openflexure-microscope
  • Feb 19 19:56
    GitLab | Joel Collins pushed 2 commits to openflexure-microscope
  • Feb 19 16:13
    GitLab | Joe Knapper pushed 2 commits to openflexure-microscope
  • Feb 19 15:50
    GitLab | Julian Stirling pushed 1 commits to openflexure-microscope
  • Feb 19 15:28
    GitLab | Joe Knapper pushed 1 commits to openflexure-microscope
  • Feb 19 13:34
    GitLab | Joe Knapper pushed 1 commits to openflexure-microscope
  • Feb 18 18:59
    GitLab | Joel Collins pushed 2 commits to openflexure-microscope
  • Feb 14 16:46
    GitLab | Richard Bowman pushed 1 commits to openflexure-microscope
  • Feb 14 14:48
    GitLab | Julian Stirling pushed 1 commits to openflexure-microscope
  • Jan 20 17:29
    GitLab | Kaspar Emanuel pushed to openflexure-microscope
  • Jan 20 17:29
    GitLab | Kaspar Emanuel pushed 2 commits to openflexure-microscope
Richard Bowman
@rwb27_gitlab
Regarding your objective, that is confusing - what's the parfocal distance (from where the sample should be to the "shoulder" of the objective)? My objectives are usually 45mm.
Also, which version of the optics module did you use in the end - the standard pre-compiled ones are for normal 160mm tube length objectives, and should fit nicely with 45mm parfocal objectives using the LS65 body and the 10mm high sample riser.
There should be some room to adjust the position of the optics module by loosening the screw and sliding it up and down - but maybe not as much as you need. Did you custom-compile your optics module in the end? I remember some discussion about that previously.
Daniel
@Dgrosen_gitlab
Hi Richard @rwb27_gitlab. I did both compile and upload. IDE displays "Done uploading". However, the serial monitor does not reply "Sangaboard v0.3". It is blank. Settings are: Board: Arduino nano, Processor: ATmega328P, Port: /dev/ce/usbserial-1410; programmer: AVRISP mkll
Daniel
@Dgrosen_gitlab
FIXED IT!!!! the codes were not uploading to the nano even though the IDE said "upload complete". This happens when you use cheap Chinese clones with a brand new MacBook Pro. So I fired up my old windows PC with USB 2.0. Had to download the drivers for the different chip (CH340G) for serial-USB communication. VOILA!!! IT WORKS!
Richard Bowman
@rwb27_gitlab
Ah, well done! Thinking about it, we have also had that issue using cheap nano boards with CH340 chips, but as I set it up ages ago and am using Windows anyway, I'd forgotten. I think for some of them we had to change the processor type too. When you say it works, do the motors move yet or have you just succeeded with serial communications?
Daniel
@Dgrosen_gitlab
The motors move. But why do you need the sangaboard? Why not let the RPi control the ULN2003 drivers?
Richard Bowman
@rwb27_gitlab
I must confess I've never tried it, but my assumption was always that the Raspberry Pi wouldn't have precise enough timings to drive stepper motors nicely... Also, by the time you've made a board with the uln drivers and power management, adding the microcontroller gives quite a bit of versatility for not much extra cost.
Julian Stirling
@julianstirling_gitlab
@Dgrosen_gitlab I am glad it now works!!
Daniel
@Dgrosen_gitlab
thanks so much. couldn't have done it without your guidance. I will post some pictures as soon as I get it all together. Still waiting for some optic components to come my way
Richard Bowman
@rwb27_gitlab
excellent, I'll look forward to seeing them!
Daniel
@Dgrosen_gitlab
which would be the suggested workflow to stitch the stack and scan images?
Richard Bowman
@rwb27_gitlab
I've used the "stitching" plugin in ImageJ, though I think @jtc42_gitlab has used a Microsoft cloud service in the past with good results. Both depend on having reasonable overlap betweent the images, though.
juliobuonfigli
@juliobuonfigli
It was simpler than we thought. Thanks for your answer @rwb27_gitlab.
Daniel
@Dgrosen_gitlab
images_20000_19400_37069.jpeg
This is so amazing!. My 1st picture captured after I assembled all components. Still missing the LED lens that may improve things a little. forgive the dirt on the slides
Daniel
@Dgrosen_gitlab
Fused.jpg
this is a fused image after a scan and stack using imagej
Richard Bowman
@rwb27_gitlab
Very nice! We've put together scripts to fix the drop in saturation at the edges of the images, but it's not yet nicely integrated. It's available
Though currently it just works with raw images, and requires some calibration...
Daniel
@Dgrosen_gitlab
Thanks. I adjusted some things and the picture now improved.
Daniel
@Dgrosen_gitlab
Hello everyone. is there a way to name the files incrementally (ie: img1, img2...) for the stack and scan function? Not sure how to make imageJ recognize the files for stitching. thanks
Daniel
@Dgrosen_gitlab
success!!!
Richard Bowman
@rwb27_gitlab
Nicely done @Dgrosen_gitlab, if only it really moved that fast! Could you share how you renamed the files? I've just used a bash script in the past, but it's not very elegant...
Rachel Aronoff
@rachelaronoff_gitlab
very inspirational discussion and video! thx for pointing me towards gitter, Richard!
Rachel Aronoff
@rachelaronoff_gitlab
got the stack and scan up! :)
Masoud
@masoud-al
for future reference : I modified ~/.openflexure/microscope_settings.yaml with the following:
plugins: ['openflexure_microscope.plugins.default.autofocus:AutofocusPlugin', 'openflexure_microscope.plugins.default.scan:ScanPlugin','openflexure_microscope.plugins.default.camera_calibration:Plugin']
For some reasonthe plugins entry was empty
Richard Bowman
@rwb27_gitlab
thanks for posting that @masoud-al - the plugins field should be populated with that automatically, so it's curious that yours wasn't - sometimes I think that can happen if something goes wrong when updating the configuration file. Joel is working on an improved plugin loading system for the next version of the software that should fix that, we're just testing it at the moment.
Richard Bowman
@rwb27_gitlab
Hi All, we're trying to tidy up the forums - we've made a general "openflexure" room and a specific fluorescence room. I hope they are both public - but do let me know if not.
Rachel Aronoff
@rachelaronoff_gitlab
thx!
Rachel Aronoff
@rachelaronoff_gitlab
Hi! I made the slide_riser_LS10 piece, thinking it might potentially be a better starting point for our 'cheek cell chip' than the ordinary sample riser piece, but I don't understand: 1) it doesn't fit an ordinary glass slide? what is the little arm for? how does it fit together? confused ... thx!
Richard Bowman
@rwb27_gitlab
it fits the 75x25mm glass slides I typically use, what size are yours? The little arm fits in the hole on the top (the non-flat side) and you then use a spring that fits between the arm and the main piece to squeeze the slide between the rounded end of the arm and the lip on the slide riser.
Daniel
@Dgrosen_gitlab
Hi Richard. Thanks. I am eternally grateful to you and your team for this incredible creation. I am using it almost everyday. I built 3 of them with different magnifications. I manually renamed the images as IMG1.jpg, IMG2.jpg, IMG3.jpg and so forth. I made a code on imageJ to process the images. The code will focus stack the images and the tile them. I would like to share it with the openflexure community. I also made a rotating slide holder to position the sample on the stage that would like to share as well
Rachel Aronoff
@rachelaronoff_gitlab
sounds good Daniel! Richard, I don't get the spring idea? can you add a picture? (will measure our slides soon!)
Rachel Aronoff
@rachelaronoff_gitlab
my slides are 75x25mm too, @rwb27_gitlab - maybe when I made the gcode from the .stl I lost the correct scale... - but the spring part may also make it work? anyway, the rotating slide holder also sounds interesting. :)
Daniel
@Dgrosen_gitlab
IMG_3443.jpg
my slides are that size too. This is how I assembled it. But the arm does not reach the slide
Daniel
@Dgrosen_gitlab
Hi. I can't compile the delta stage with openscad. I get this error
RROR: CGAL error in CGAL_Nef_polyhedron3(): CGAL ERROR: assertion violation! Expr: e_below != SHalfedge_handle() File: /Users/kintel/code/OpenSCAD/libraries/install/include/CGAL/Nef_3/SNC_FM_decorator.h Line: 427
vighnesh mayekar
@vigs98_gitlab
@nikitajes hiii
@nikitajes I am also final year students . I have some doubts regarding this project . will you please guide me for this stuff .. is any way to contact with you?? plz rply
Richard Bowman
@rwb27_gitlab
image.png
@rachelaronoff_gitlab @Dgrosen_gitlab I've scribbled on the place where the spring goes - does that make it clearer? I'm afraid I can offer no advice on where to get a suitable spring, as I made this part in Tanzania, with the spring that our Tanzanian collaborators said they could reliably get hold of! If you find a reliable source for the spring (or even figure out the correct dimensions) please do post it here :)
I should also tell myself off for posting here - we are trying to move over to the new gitter room for the OpenFlexure community
Please move to the new gitter room
vighnesh mayekar
@vigs98_gitlab
@rwb27_gitlab can you please explain how does the movement of image occurs in the microscope. I am using the motor for control.... but I am not getting the linkage between motor ..
Richard Bowman
@rwb27_gitlab
@vigs98_gitlab could you ask again in the new gitter room?