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crabrock
Aug 2, 2002

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oh boy, good tech support!

Day 0:

me posted:

I took stack images with 900 images with Neurolucida. When I tried to save the file as a .tiff image stack, both of the files maxxed out at 2,102,674 kb, and will not open (it says they are corrupt). The program appeared to hang while I was saving it, but came back online and didn't have any popups or errors stating that the file was bad, though it did crash when I tried to do the 3d view.

Is there some upper limit that I'm hitting here? should I be using a file format other than tiff for these stacks? I need the big stacks because I am importing the files into NeuroLucida360 to do cell anatomy tracing.

Thanks,

Day 6:

quote:

Dear crabrock:
The first thing the programmers would like to check is whether you might be running out of disk space. They get messages like that when there is not enough room to save; and that would go along with the fact that both files stopped at exactly the same size.
Thank you,
Dr. Daniel Peruzzi I Research Liaison

quote:

No, both files were saved in the same computer with plenty of space, so that is not the issue. I wouldn't have been able to save another 2gb file if I was out of space for the first one.

Additionally, we have 140gb free on this hard drive.

The program just stopped saving the file. It "completed" and went back to working like normal. No errors or anything.

I was digging through the settings to see if I can find any reason this is happening. Our"video memory" is 2 gb. Could this be a reason? Are the saved stacks processed with video memory?

Day 8:

quote:

Thank you for letting us know there is plenty of room on the hard-drive. I have also forwarded the idea about the video memory to the programmers working on this and we have the file that did not save to completion. I will be away at the Society for Neuroscience meeting until the week of Thanksgiving, but the programmers will be here and hopefully make progress. If you need help in the interim, please use support.mbfbioscience.com.

Thank you,
Dan

quote:

Hi Dan,

Thanks for the update. Will they be in direct contact with me? We'd really like to get it figured out ASAP, since it's holding up our experiment, and if it's just buying a higher memory video card we can do that.

Day 9:

quote:

Dear Dr. Rock:
Thanks for letting me know about the urgency. I have forwarded this problem to Head of Tech Support, Zoltan. He is not attending the Neuroscience conference.
Sincerely,
Dan


(lol at getting so formal all of a sudden)

Day 14:

quote:

Hi crabrock– Dan is at SfN and asked me to follow up internally and with you. One question that came up is: Is there sufficient disk space on the system to save your 6Gb file?
Thank you,
/zoltan

:bang::bang::bang::bang::bang::bang::bang::bang::bang::bang:

i answered the question myself after some more googling. apparently a tiff can only save 2gb files. I had erroneously landed on some page saying the limit was much, much higher (but that's bigTiff). In two weeks they are still asking me the same stupid question they started with, which doesn't even make logical sense given the information i provided them.

Tiff/jpg are the only formats this program will save images as. each slice in the stack is 16MB and there doesn't appear to be any way to decrease the resolution. obviously i'm not going to save high resolution microscopy photos as jpg...

glad i wasted 2 weeks on this instead of just using another program to capture the images.

crabrock fucked around with this message at 18:02 on Nov 14, 2017

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crabrock
Aug 2, 2002

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i sent them a slightly passive aggressive response about how i just moved on to a more appropriate piece of software and told them the info i'd found and then magically within 5 minutes the responded back with

quote:

1. Save in .JPX format instead of .TIF.

Our first recommendation to customers saving large files acquired and analyzed in our software should be to use the .jpx image file format (keep all the resolution in a much smaller image file). This will also help when opening it in NL360 (also it couldn’t hurt to mention when using large files in NL360 that it is best to zoom in on the image in the 2D window and then open the 3D window – this will allow it to open smaller areas of the image in the 3D making it possible to work with large images with a less beefy computer – BUT saving as .jpx may make it possible to open the entire thing in NL360 3D). MBFJPeg2000 - .jpx

2. Our records show you are using current versions of both NL and NL360, v2017.02.2 and v2017.01.3 respectively. Please verify this is the case.
3. Are you acquiring a single image stack or a 3D Virtual Tissue?
4. We are QA testing an updated library that will allow for .TIF files larger than 2GB. It is not ready yet.

THANKS FOR YOUR FIRST RECOMMENDATION 2 WEEKS LATER

crabrock
Aug 2, 2002

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hope nobody's got a grant deadline coming up :\

I did my postdoc interviews after trump got elected and it actually played a part in my decision to go to a private university instead of a public university. I mean, it was a small part, but two positions had a lot of appeal and I could have been happy at either, I think.

crabrock
Aug 2, 2002

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when u do a 384 well PCR by hand but use the mouse primer instead of the rat primer :suicide:

crabrock
Aug 2, 2002

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my coworker dropped a whole 24 well plate of my best hippocampal sections and i replaced them and then FISH didn't work anyway :(

crabrock
Aug 2, 2002

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anybody have any experience with xraying fixed tissue?

i only ask because a friend flew with some brain sections, and now they seem to almost be repelled from our superfrost+ slides and they took like 10 times longer to mount than they should have and it was a struggle the entire time. I know you can use microwaves to fix tissue, and was wondering if an Xray would change something about them? Or it could have been the pressure of the plane... i dunno. It's just strange.

Staining turned out awesome though so whatever happened to them didn't ruin them at least.

crabrock
Aug 2, 2002

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my lab has solved this by printing a label with the password and sticking it to the monitor

security theater!

crabrock
Aug 2, 2002

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one of my labmates almost died from a faulty fume hood and the school lawyers "made" her sign a bunch of things saying she wouldn't sue the school and she signed all of them because she felt like it was her fault somehow.

crabrock
Aug 2, 2002

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where are you moving?

crabrock
Aug 2, 2002

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clark?

i always pity the people working in there, everybody can just loving see u

crabrock
Aug 2, 2002

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lol no. the power never went off in our building when that happened i guess the hospital has backups.

crabrock
Aug 2, 2002

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never underestimate the importance of keeping poo poo clean/aliquoted. i simply cannot believe the amount of filth/contamination i see in labs all over the place.

crabrock
Aug 2, 2002

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i left my lab notebook in the animal surgery room too long and now it smells like rat piss

crabrock
Aug 2, 2002

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Artonos posted:

If we're talking accidentally smelling stuff. I got a nice whiff of chloroform once. It burned the nostrils pretty bad and was a pretty small amount.

a light whiff of chloroform smells kinda sweet. any more though and it's downright nasty.

crabrock
Aug 2, 2002

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Does anybody know of a small glass insert i can stick in a 1.5 ml eppendorf tube? I've tried searching and can't find anything, but it seems like this has to be something somebody has wanted before... And I'm tired of cutting them myself.



crabrock
Aug 2, 2002

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I don't think so. The mini slides have deparaffinized FFPE tissue sections on them. I need them to be flat for imaging and downstream stuff.

The ones i posted work well, i just don't like making them myself.

crabrock
Aug 2, 2002

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I'm using a diamond tip glass scorer and cutting them from regular glass slides (i want the positive charge properties).

I can get 4-5 ok mini slides per slide. It's just a pain in the rear end and I'd like a lot more and not have to wash the ones I've already made. I'd probably go through hundreds (I'm in R&D and i have a lot of failures).

Maybe my company will just order me some custom ones but wanted to make sure nobody already made them.

crabrock
Aug 2, 2002

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Johnny Truant posted:

I made the jump from academia to industry recently and jfc. This is so much better. Like infinitely better. :coolslime:

seconded

i hosed up a sequencing run and my boss was so understanding of it and we went over the thing i did wrong and then immediately planned our next one. there was no weird punishment or fretting over how much i'd just cost them or suggesting that it was because i'm stupid. just "well now you know for next time, which will be thursday"

such a weird change from all the stress of messing up new assays in my previous labs

crabrock
Aug 2, 2002

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i'm having some issues with an assay. about half the time it works, and the other half the time it doesn't. nobody else on my team has this issue. today another member watched me do every single step of the two day process, while doing it alongside of me. when we finished hers worked and mine didn't.

we didn't figure out what i'm doing wrong, but i've successfully vexed another person who is now confused as hell :)

crabrock
Aug 2, 2002

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my work has an airhorn taped to the wall that says "use in case of emergency" but it fell off the wall and i don't know where it went. that's ok i'm real close to the door.

crabrock
Aug 2, 2002

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Douche4Sale posted:

I had an undergrad once who was helping me with immunostaining. I happened to glance over and see him standing at the sink, running the tissue sections under the water and squirting hand soap on them.

I was so focused on the “tricky“ steps that I just mentioned the washing steps in passing. When he got to the first “wash“ step in the protocol, he decided he knew the best way to wash something...

he's just permeabilizing for you in a cheaper way.

crabrock
Aug 2, 2002

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i always figured Falcon was the NameBrand stuff made by Corning and the highest likelihood of being good, with absolutely no evidence or data to back that up.

if you had problems with RNA in their stuff it's probably because you thought too hard about the RNA, and it degraded out of shame.

crabrock
Aug 2, 2002

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what's the best solution for just magnetic bead cleanup. that's the part i hate the most and we have to do it 4x for our prep.

crabrock
Aug 2, 2002

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i'm gud enough it's just so boring :cry:

crabrock
Aug 2, 2002

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those look cool but our throughput is probably too low to justify their use. i'm in R&D and we usually are only running 2-8 samples per run, but almost every day I'm doing a library prep and it's the most monotonous and boring part of my job.

do you have any knowledge about low throughput NGS library automation, like this thing? https://www.perkinelmer.com/product/bioqule-ngs-system-cls155700

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crabrock
Aug 2, 2002

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MAGNIFICENT






here, chat GPT made this for you. I helpfully had it send a slack message every time you eject a tip to notify the people who are bugging you.

code:
import requests

class ElectronicPipette:
    def __init__(self, min_volume, max_volume, slack_webhook_url):
        self.min_volume = min_volume
        self.max_volume = max_volume
        self.current_volume = min_volume
        self.slack_webhook_url = slack_webhook_url
        self.tip_attached = True

    def increase_volume(self, increment):
        if self.tip_attached:
            new_volume = self.current_volume + increment
            if new_volume <= self.max_volume:
                self.current_volume = new_volume
                print(f"Volume increased to {self.current_volume}µl")
            else:
                print("Cannot increase volume: Maximum volume exceeded.")
        else:
            print("No tip attached. Please attach a tip before adjusting the volume.")

    def decrease_volume(self, decrement):
        if self.tip_attached:
            new_volume = self.current_volume - decrement
            if new_volume >= self.min_volume:
                self.current_volume = new_volume
                print(f"Volume decreased to {self.current_volume}µl")
            else:
                print("Cannot decrease volume: Minimum volume exceeded.")
        else:
            print("No tip attached. Please attach a tip before adjusting the volume.")

    def load_fluid(self):
        if self.tip_attached:
            print(f"Loading {self.current_volume}µl of fluid.")
        else:
            print("No tip attached. Please attach a tip before loading fluid.")

    def dispense_fluid(self):
        if self.tip_attached:
            print(f"Dispensing {self.current_volume}µl of fluid.")
        else:
            print("No tip attached. Please attach a tip before dispensing fluid.")

    def eject_tip(self):
        if self.tip_attached:
            self.tip_attached = False
            print("Pipette tip has been ejected.")
            self._send_slack_message("A tip has been ejected.")
        else:
            print("No tip attached to eject.")

    def _send_slack_message(self, message):
        data = {'text': message}
        response = requests.post(self.slack_webhook_url, json=data)
        if response.status_code == 200:
            print("Message sent to Slack.")
        else:
            print("Failed to send message to Slack.")

# Example usage
pipette = ElectronicPipette(min_volume=10, max_volume=1000, slack_webhook_url='https://hooks.slack.com/services/YOUR/SLACK/WEBHOOK')
pipette.load_fluid()
pipette.increase_volume(50)
pipette.dispense_fluid()
pipette.eject_tip()

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