En biología usamos un microscopio, pero en química casi nunca.

Yes. Here en means in in the sense of in the subject/field of.

• En biología = In biology
• En química = In chemistry

Spanish often uses en to talk about school subjects, areas of study, or contexts:

• En matemáticas, usamos calculadora. = In maths, we use a calculator.
• En historia, leemos mucho. = In history, we read a lot.

So here it means in biology class / in the field of biology, not physical location.

When Spanish talks about school subjects or academic disciplines in a general sense, it usually does not use the article.

So:

• en biología
• en química

are the normal forms.

Using la would usually sound more like biology as a field/topic itself, not the school-subject context. For a learner, the safest rule is:

• With subjects in general, usually no article
• Example: Me gusta la biología can be correct because now biología is the thing you like
• But en biología is the usual expression for in biology

Usamos means we use, so the speaker is including themselves in the statement.

• usamos = we use
• usan = they / you all use
• se usa = it is used / one uses

This sentence sounds like someone talking from the perspective of a group, such as students, scientists, or people in a class:

• En biología usamos un microscopio = In biology we use a microscope

If the speaker wanted a more impersonal, general statement, they could say:

• En biología se usa un microscopio = In biology a microscope is used / people use a microscope in biology

Both are possible, but usamos is more personal and direct.

Because Spanish usually leaves out subject pronouns when they are not needed.

The ending of the verb already tells you who the subject is:

• uso = I use
• usas = you use
• usa = he/she/it uses
• usamos = we use
• usáis = you all use
• usan = they/you all use

So usamos already means we use.
Adding nosotros is only necessary for emphasis, contrast, or clarity.

• En biología usamos un microscopio = neutral
• En biología nosotros usamos un microscopio = more emphatic, like we use one

In Spanish, countable singular nouns usually need an article or another determiner.

So:

• un microscopio = a microscope
• el microscopio = the microscope

Saying just usamos microscopio would sound incomplete or unnatural in standard Spanish.

Spanish often includes the indefinite article where English also does:

• Tengo un libro
• Necesitamos una mesa
• Usamos un microscopio

Because Spanish often leaves out repeated words when they are easy to understand from context.

The full version would be:

• En biología usamos un microscopio, pero en química casi nunca usamos un microscopio.

But that sounds repetitive, so Spanish omits the repeated part:

• pero en química casi nunca

The listener understands that the missing idea is:

• usamos un microscopio

This kind of omission is very common in both Spanish and English:

• In biology we use a microscope, but in chemistry almost never.

Casi nunca means almost never.

It is made of:

• casi = almost
• nunca = never

So together:

• casi nunca = hardly ever / almost never

Examples:

• Casi nunca voy al cine. = I almost never go to the cinema.
• Casi nunca llueve aquí. = It almost never rains here.

In your sentence, it means that in chemistry the use of a microscope is very rare.

Yes, Spanish allows some flexibility, but the position here is very natural.

Original:

• En biología usamos un microscopio, pero en química casi nunca.

This works because casi nunca modifies the omitted idea usamos un microscopio.

You could also say:

• En biología usamos un microscopio, pero casi nunca en química.

But the original sounds more balanced and natural because it contrasts:

• en biología
• en química

So the structure helps highlight the difference between the two subjects.

Because in Spanish, names of school subjects, languages, and academic disciplines are normally written in lowercase.

So:

• biología
• química
• español
• historia

This is different from English, where some subject names are often capitalized depending on style.

So in Spanish:

• Estudio biología.
• En química hacemos experimentos.

Lowercase is the normal spelling.

They have written accents because Spanish spelling rules require them.

• biología
• química

The accent mark shows which syllable is stressed:

• bi-o-lo-GÍ-a
• QUÍ-mi-ca

These accents are part of the correct spelling and should always be written.

For learners, it is useful to remember:

• Many words ending in -ía have an accent: geografía, biología, tecnología
• química also needs the accent to show the stress pattern

Un microscopio is the indefinite article, so literally it means a microscope.

In this sentence, it refers to the instrument as a type of tool, not one specific microscope. So the natural idea is:

• In biology we use a microscope

It does not normally mean one particular microscope already known to both speaker and listener. If Spanish wanted to refer to a specific one, it would more likely use:

• el microscopio

So:

• un microscopio = a microscope, as a general tool
• el microscopio = the microscope, a specific one

It could be understood either way, depending on context.

It can mean:

• In biology class we use a microscope, but in chemistry almost never or
• In the field/practice of biology we use a microscope, but in chemistry almost never

Without more context, both are possible. The structure en biología / en química works well for either:

• school subjects
• academic disciplines
• scientific fields

In everyday learning materials, many people would first understand it as referring to school subjects.