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python-microscope / microscope

Python library for control of microscope devices, supporting hardware triggers and distribution of devices over the network for performance and flexibility.
https://www.python-microscope.org
GNU General Public License v3.0
71 stars 41 forks source link

script to automate whole slide acquisition #249

Open Divyadeep00 opened 2 years ago

Divyadeep00 commented 2 years ago

Hello everyone,

I have leica microscope with camera. Model no. Dm 6000 B. I want to make a image, which represent full slide (mosaic of images of every unit area). But I want this to be automatic. Is there any script or how to make such script.

Looking forward to hearing from you soon.

carandraug commented 2 years ago

Such a script can be written but this is typically done through some GUI program (such as cockpit). However, there is currently no support for that camera.

Divyadeep00 commented 2 years ago

Thank you for replying @carandraug.

ok sir, if such support comes, please mention it. If you can suggest some another way to automate whole slide acquisition. It will be helpful.

Thank you

iandobbie commented 2 years ago

We have not investigate the Leica frames at all but I'm afraid our previous efforts with major manufactures frames have been a total dead end. Both Zeiss and Olympus require an MTA to be signed to get access to the relevant libraries to interface with their scopes. We are not willing to do this as it restricts us distributing source to connect to their driver.

If this is different for Leica, thats great news, I would love to hear that.

Divyadeep00 commented 2 years ago

I do not have much programming knowledge, so maybe I am not the right person for this. By the way, thank you for your reply.

Divyadeep00 commented 2 years ago

But let us make this for Leica and Olympus because these two are widely used microscope frames, at least in India; if these are commonly used in the entire world, then this python-microscope will flourish very quickly and be helpful for many educational institutes because they don't have to pay for such costlier software of Leica.

Thank you

iandobbie commented 2 years ago

Such a script can be written but this is typically done through some GUI program (such as cockpit). However, there is currently no support for that camera.

I think the DM6000 is a complete integrated systems with motorised microscope stand and camera sold as a package. Not sure it has motorised stage though.

Divyadeep00 commented 2 years ago

yeah, I can control the microscope from Leica LAS V4.2 software, but the mosaic system is not there. I think the motorised stage is there.

If you can suggest a way to make the whole slide acquisition, I am very thankful for you.

carandraug commented 2 years ago

I do not have much programming knowledge, so maybe I am not the right person for this. By the way, thank you for your reply.

What @iandobbie means with "require an MTA to be signed to get access to the relevant libraries to interface with their scopes" is that the only way to control such microscope is if Leica tells us how and they only tell us if we don't write software for others which makes the whole thing pointless.

Anyway, I thought this discussion really belongs to issue #248 and that this was about having, probably on documentation, a script example for whole slide acquisition. If not, then this is a duplicate of #248.

Divyadeep00 commented 2 years ago

Yeah, I raised this issue only for the script for the whole slide acquisition. and issue #248 was to know the support of Python microscope on Leica.

iandobbie commented 2 years ago

You might find some way to do this on image.sc. A thread to start with might be https://forum.image.sc/t/micro-manager-for-leica-dm6000b-with-ctr6000-controller/68582