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In case someone wants to cite this repo we need a DOI badge from our Zenodo archive or the biorxiv preprint.

@b286 would you mind to take care of that?

I am working on a raman microscope, one of the components is a spectrophotometer.

I decided to follow the current working guide but doing so will not generate any spectra.

The camera or imaging module must be perpendicular to the diffraction grating.

In my case I placed a perpendicular 45 degree mirror so spectral image is reflected on top where a phone or webcam imager can be conveniently placed.

Think about the 6-screw-magnetic-slide idea.

Build any of the setups from APPLICATIONS and add your results to the respective README file and IMAGES folder.

Proposed format:

• date (DD.MM.RR) of submisson
• your name and institution (if applicable)
• short comment of your results
• image of your setup - UC2_results_setup_DDMMRR.jpg or .png in the respective IMAGES folder
• images you took using your setup - UC2_results_DDMMRR.jpg or .png in the respective IMAGES folder

@renerichter @strolch101 can we provide a minimal working example?

After reading your paper, I ordered the XY stage from Aliexpress. Along with the stepper motor connectors it has extra electronics parts, which I believe or end stops. Could you please confirm what they are for. The flex ribbon cable seems a better value, so can we find a connector for this?

The readme in openKoehler is shown as the readme for openSIM

Maybe there are some tools in the web who do that automatically?

A tool which reads the database and suggest which parts to print with links would be cool!

We need a list with available low-cost components which can be used for our setup. Should be found in our Documents folder.

Ask @strolch101 to add a download link to images.

Should we also think about this link here:
rwb27/openflexure_microscope_software#10 (comment)

It gets rid of the Shading correction at the rim of the cameras sensor.

We should provide different holes for magnets to give people to adjust it according to their (non)-calibrated printers. Maybe a Thingiverse configurator could do the job - or just a list of different STLs. Since we reduce it to only one part rather than 1x3, 2x5, etc. we don't need to do that for all the baseplates.

Under "3D printing parts", the LED-Matrix Adapter STL is a broken link.

It points to
./STL/20_Cube_insert_LED_holder.stl
instead of
./STL/30_Cube_LED_Array_v0.stl

I figured, that the current openISM documentation is not up-to-date and in-line with the manuscript.
@ranranking would you mind helping me to update it? I have updated the structure of the openSIM. I would like to have the two versions similar. Would be great. Thanks :)
Currently, everything is in the v3 branch.

My adblocker refused to open useetoo.org because of the trackers and known malware distributors being accessed in by the website. This is the first time I recall this happening. I allowed the trackers temporarily and landed at a "prize" page for my number of google searches. Has your web site been hacked?

First I would like to express my gratitude for the team who made this modular microscopy possible.

I was inspired to purchase a 3d printed to build my raman microscope. I have my spectrophotometer prototyped using lego blocks and on my way 3D printing the microscope components.

I purchased stainless steel (M3-0.50 x 12mm) on Amazon and the biggest surprise is it is not magnetic. This might be a potential issue for future makers, so can we add a list of tested and suitable materials specification indicating they can be magnetized? I see in the site a link to a European source but it would be useful to detailed out specific metal characteristics and warning that some stainless steel and zinc coated screws cannot be magnetized effectively.

Add the corresponding PNGs to the schematics. Simply export it from Fritzing and add to README.

• eyepiece: yes or no?
• sample holder - old version or new one with screws+magnets?
• amount of baseplates: planned 8, do we want to sandwich it? -> then 16
• sample mounting in smartphone microscope: is it clear and okay now?
• lens holder: does the new version work well, stays closed?
• which spring length/diameter for the z-stage?
• z-stage working well?

Write a small document which explains the setup of a XYZ-stage with some images.

The pattern generation plugin from fairSIM is not on their github anymore or i didnt find the right path to find it.
pattern-generation software

We should add some spacer between the insert and the cube to have it centered.

Instead of having an expensive hard to get cylindrical lens, I tested a plane-convex plastic slab which is made out of Plexiglas (R) with an refractive index of 1.48 I suppose. You can get it very cheap at ebay

This is the slab with a radius=15mm, so should give a focus of roughly f'=15mm`

Here it is hold in the holder:

And the STL-file
20_Cube_Insert_Lens_Cylindrical_Plexiglas_glassslab_v3.zip

@b286 what do you think, should we have this as an additional module?

Hi, I just printed all the files in UC2-GIT/CAD/ASSEMBLY_CUBE_RaspiCam_v2/STL but don't understand how the sensor is supposed to be held at a particular postion without play. Is there some way how the 20_Cube_Insert_RaspiCam.stl part is held rigidly within the cube that I am missing?

Also, when I look closely at this picture from the inline holography example (zoomed in and annotated below), it looks to me like the RaspiCam insert is rendered a few mm lower than is physically possible. In particular, if you look at how the gray camera insert overlaps the dark green lid, it looks like the lid is occupying the same volume as the insert, which is physically impossible.

If I look at the Camera Cube readme for help, this unfortunately does not clarify the situation for me. Also, the last image shows the sensor held by only a single screw, so perhaps a rigid mounting is not very important for this application.

Based on the work by the openflexure team and @AlecVercruysse, we want to have an online configurator which allows the creation of ready-to-print .zip-files of UC2 Applications which are always up-to-date.

The script which generates JSON files for each APPLICATION now successfully converts the excel sheet into a useful JSON-file. It's still experimental and can be found here.

@AlecVercruysse I still didn't consider the ability to conditionally choose options. I think therefore I need to get a better idea of what it could be. Do you mean something like camera: A or camera: B and lens: A or lens: B in one Application?

Also, would you mind to see if the structure fits what you would expect in your online configurator?
Anyway, I'll try to have a look at your VUE code and see if I have any chance understanding it ;)

Many of the easily available lenses (e.g. form Ajax Scientific have 50 mm diameter. It would be useful to also be able to mount them.
They just about fit in the standard cube, but a different mount would be needed. It is not so important to have to full size as a transmitting surface.
Can one make a design for a variable holder for big lenses?

In addition it may also be interesting to make a design for a holder that can even deal with 10 cm lenses at a large distance from the front cube, for example to build a telescope with a 10cm entrance lense.

Hello,

Will the inventor files be released for any of these modules? Converting an STL to a solid body makes for a generally unconstrained and tough file to edit.

I'm asking because I need to design an objective holder for the z-stage that fits the objective we use, and I would like to simulate the whole assembly to ensure alignment.

Thanks!

Perhaps we could add a short list of recipes for sample preparation with images for those who have never dealt with this.
@RainerHeintzmann you could give an example of preparing the flowers for example
@ranranking @b286 - perhaps some cools stuff from your work? Cheek cells and fibers are nice samples too.

What do you think?

Most cheap optics are with RMS threadings, but I guess we should make this somehow adaptable - at least the part which slides through the z-stage. @b286 do you have a good way of doing that? Maybe something in Thingiverse?

Perhaps it should look more like this rather than a full radial hole?

@b286 any idea?

This page:
https://github.com/bionanoimaging/UC2-GIT/tree/master/CAD/ASSEMBLY_CUBE_Z-STAGE_mechanical_v2
says the parts can all be printed without support.
I printed the focus linear bearing flexure:
https://github.com/bionanoimaging/UC2-GIT/blob/master/CAD/ASSEMBLY_CUBE_Z-STAGE_mechanical_v2/STL/Assembly_Cube_Z-Focus_Linearbearing_1x1_v4_20_focus_inlet_linearflexure_v4_7.stl

and while the piece prints OK without support in the default orientation, the print quality is a bit low (the long bridges have lots of extra squigglies). I don't want to add support on the bridging flexures, since it would be tough to remove. Is there a way to put some internal supports in that can be easily removed to improve those?

BTW I'm using a Prusa MK3S with PETG, but I can also do ABS and PLA.

If the Fluomodules' LED is turned on above a certain value, it blocks the I2C connection. Probably the Arduinos are under-voltaged.

Solution: Use only 2 LEDs instead of 4!

It's not clear which wire go where.

When do we merge the v3 branch into master? What is left to be done before that?

• We should keep a link to the pre-merge point of the repository history somewhere on sight, at least for some time, for people who might still be working with v2.

• The video updates by @edabngl can be done after merging the branch

• The SIM+ISM documentation @ranranking What's the state?

Anything else?

We want to be user-friendly but to improve on that, we need users ;)

Start with the UC2 project by following our Tutorials of the TUTORIALS section. Suggest improvements to the Tutorials if the instructions are not clear enough, more images are needed, something is not as obvious as we thought...

General issues

• Lenses: how shall we take into account that there are different holders for different lenses and that the user might need to create his own?

GitHub

• for v3 I omitted the version from the name of the module, since renaming everything everywhere is a hassle and this will save time in the future. However, all the modules that existed in git with ‘_v2’ in their name now appeared extra in the configurator and their folders also appeared again in the git CAD folder, with the only file in them being the ‘config.json’. The ‘_v2’ options in the configurator contain the v3 inserts that correspond to the module but not the cube and lid

STLs

• is it necessary for each part to end with _v3? The .ipts and hence the generated .stls for which it matters do have it in their name already
• The renaming is a very good solution, although except for changing the prefix from UC2_v3 to UC2 only and cutting off the suffix number that Inventor creates when generating the file, I don’t see much difference. The “main” file names (without the prefix and suffix number) were matched between the excel and RAW/STL folder. Wouldn’t it be then enough to just cut the suffix numbers?

Excel sheet

• there must be some confusion between the v2 and v3 version of the excel sheet. or did you use a different tab than v3?
• the configurator doesn’t take into account the amount of parts stated in the excel sheet - shall the multiple parts be added as extra lines?
• by making all the OPT parts default, the user might get more STL files than he needs - the question is whether printing some redundant parts makes him unhappy or whether it makes him unhappy not to find the parts in the zip folder when he needs them. I can’t decide what’s better

Configurator (general)

• it would be nice to have a ‘clear all’ option for the case when one added a lot off different modules and got lost in it

Long-time ago we were thinking about recycling 3D printing material. One service is this one.
I think that's fairly expensive. Maybe we can find some local alternative?

Any ideas @RainerHeintzmann @b286?

We should definitely add some shielding elements which reduce the stray-light between the individual parts.

I have written a small Python script that handles proper renaming of the STL files in the /CAD/RAW/STL folder. It is inside the same folder and calls convertname.py
Please have a look there @b286. The naming convention must be reflected in the Excel sheet as well. Thank you.

Add links to: learning 3D printing, starting with Raspberry Pi, and so on.
"When introducing a method always provide the option to learn how to do it"

10_Base_v2.stl, Assembly_base_4x1.stl, and Assembly_base_4x2.stl in Master aren't scaled properly. I had to scale 39.37% to print at the proper scale. There may be more as I've not tested them all.

Maybe we can get some inspiration in this publication
https://www.degruyter.com/downloadpdf/j/cdbme.2018.4.issue-1/cdbme-2018-0065/cdbme-2018-0065.pdf

More detailed guidelines would help!
Hints for basic raspi commands (for just setting up the camera etc.) - taking image, ....

Hi,

Just discovered this project. It is really amazing! Could you please let me know if it's possible to use the spiral or fixed lens holder for tube objective lens?

Many thanks!

Jerry

Do we want to have the smartphone holder slidable, or would it be even better to stack them to the pins of the new cubes like the plate for the LED I showed you recently?
@b286

Hello,

What is the purpose of the Assembly_Base_Connector_4? Is it just the 4u version of 00_Connector_Baseplate, meant for 3D designs? The readme describes it as "length of 4 baseplate units" but nothing more.

I am asking because, if I was constricted to a 120x120mm print bed, but wanted a 4x2 baseplate, I would need to connect two 2x2 prints. I know am able to construct the 2x2 base using 10_Base_v2. Is the purpose of the holes along the x and y axes meant to facilitate the connection of these baseplates, with m3 screws and nuts?

Additionally, what is the naming scheme behind your CAD files, particularly the two digit number in front?

Thank you for the help!

The additional part which fixes the mirror is too small to hold the mirror. We need to improve that!

For parts like the AlliedVision camera, we should perhaps design inserts that are an inner cube rather than just a plate. This could help the part to not move around.
What do you think @b286 ?

Insert is wiggeling around inside the cube. We should have more screws making it more stable.
Also: We should use screws with heads instead of the worm screws to mount it inside the cage

A short document which give a brief introduction about the following aspects:

• Keppler Telescope
• Galileo Telescope

What to include:

• Brief Description
• Photos
• CAD files
• CAD rendering

Hello,

It seems that MDK/CAD/Assembly_Cube_Baseplate_1x1/ only contains the inventor project files that pertain to v0 of the baseplate, while the baseplate folder in CAD/ contains v2 of the baseplate. Is there a chance you can provide the inventor project files for v2?

Related to this issue, since there seem to be many copies of what seem to be the same file in every repository (e.g. the STL files pertaining to each module in the Applications), are there plans to consolidate and "future proof" the design files by symlinking (or similar) to the files in the CAD folders? Or do you choose not to in case there are backwards compatibility issues with new versions in the future?